chr17-35117045-AT-A

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_002878.4(RAD51D):c.263+1455delA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000845 in 1,608,548 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.000079 ( 0 hom., cov: 32)

Exomes 𝑓: 0.000085 ( 0 hom. )

Consequence

RAD51D
NM_002878.4 intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:2

Conservation

PhyloP100: 0.852

Publications

0 publications found

Variant links:

Genes affected

RAD51D (HGNC:9823): (RAD51 paralog D) The protein encoded by this gene is a member of the RAD51 protein family. RAD51 family members are highly similar to bacterial RecA and Saccharomyces cerevisiae Rad51, which are known to be involved in the homologous recombination and repair of DNA. This protein forms a complex with several other members of the RAD51 family, including RAD51L1, RAD51L2, and XRCC2. The protein complex formed with this protein has been shown to catalyze homologous pairing between single- and double-stranded DNA, and is thought to play a role in the early stage of recombinational repair of DNA. Alternative splicing results in multiple transcript variants. Read-through transcription also exists between this gene and the downstream ring finger and FYVE-like domain containing 1 (RFFL) gene. [provided by RefSeq, Jan 2011]

RAD51D Gene-Disease associations (from GenCC):

breast-ovarian cancer, familial, susceptibility to, 4
Inheritance: AD Classification: STRONG, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), Genomics England PanelApp
hereditary breast ovarian cancer syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
hereditary breast carcinoma
Inheritance: AD Classification: LIMITED Submitted by: ClinGen

RAD51D links:

ENSG00000267618 (HGNC:):

ENSG00000267618 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -6 ACMG points.

BP6

Variant 17-35117045-AT-A is Benign according to our data. Variant chr17-35117045-AT-A is described in CliVar as Likely_benign. Clinvar id is 492413.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-35117045-AT-A is described in CliVar as Likely_benign. Clinvar id is 492413.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-35117045-AT-A is described in CliVar as Likely_benign. Clinvar id is 492413.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-35117045-AT-A is described in CliVar as Likely_benign. Clinvar id is 492413.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-35117045-AT-A is described in CliVar as Likely_benign. Clinvar id is 492413.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-35117045-AT-A is described in CliVar as Likely_benign. Clinvar id is 492413.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-35117045-AT-A is described in CliVar as Likely_benign. Clinvar id is 492413.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-35117045-AT-A is described in CliVar as Likely_benign. Clinvar id is 492413.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-35117045-AT-A is described in CliVar as Likely_benign. Clinvar id is 492413.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-35117045-AT-A is described in CliVar as Likely_benign. Clinvar id is 492413.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-35117045-AT-A is described in CliVar as Likely_benign. Clinvar id is 492413.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-35117045-AT-A is described in CliVar as Likely_benign. Clinvar id is 492413.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-35117045-AT-A is described in CliVar as Likely_benign. Clinvar id is 492413.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-35117045-AT-A is described in CliVar as Likely_benign. Clinvar id is 492413.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-35117045-AT-A is described in CliVar as Likely_benign. Clinvar id is 492413.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-35117045-AT-A is described in CliVar as Likely_benign. Clinvar id is 492413.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-35117045-AT-A is described in CliVar as Likely_benign. Clinvar id is 492413.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-35117045-AT-A is described in CliVar as Likely_benign. Clinvar id is 492413.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-35117045-AT-A is described in CliVar as Likely_benign. Clinvar id is 492413.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-35117045-AT-A is described in CliVar as Likely_benign. Clinvar id is 492413.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr17-35117045-AT-A is described in CliVar as Likely_benign. Clinvar id is 492413.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAd4 at 12 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAD51D	NM_002878.4 link	c.263+1455delA		intron_variant	Intron 3 of 9	ENST00000345365.11	NP_002869.3	O75771-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAD51D	ENST00000345365.11 link	c.263+1455delA		intron_variant	Intron 3 of 9	1	NM_002878.4	ENSP00000338790.6		O75771-1
ENSG00000267618	ENST00000593039.5 link	c.3+4245delA		intron_variant	Intron 1 of 6	2		ENSP00000466834.1		K7EN88

Frequencies

GnomAD3 genomes

AF:

0.0000790

AC:

AN:

151944

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000176

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000366

AC:

AN:

246148

AF XY:

0.0000374

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000808

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000851

AC:

124

AN:

1456604

Hom.:

Cov.:

AF XY:

0.0000732

AC XY:

AN XY:

723756

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

33360

American (AMR)

AF:

0.00

AC:

AN:

44468

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

25880

East Asian (EAS)

AF:

0.00

AC:

AN:

39586

South Asian (SAS)

AF:

0.00

AC:

AN:

86050

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53322

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5738

European-Non Finnish (NFE)

AF:

0.000112

AC:

124

AN:

1108034

Other (OTH)

AF:

0.00

AC:

AN:

60166

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.481

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0000790

AC:

AN:

151944

Hom.:

Cov.:

AF XY:

0.0000809

AC XY:

AN XY:

74202

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

41348

American (AMR)

AF:

0.00

AC:

AN:

15238

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3462

East Asian (EAS)

AF:

0.00

AC:

AN:

5188

South Asian (SAS)

AF:

0.00

AC:

AN:

4830

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10568

Middle Eastern (MID)

AF:

0.00

AC:

AN:

316

European-Non Finnish (NFE)

AF:

0.000176

AC:

AN:

67992

Other (OTH)

AF:

0.00

AC:

AN:

2090

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.000142

Hom.:

Bravo

AF:

0.0000567

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Hereditary cancer-predisposing syndrome

Benign:1

Oct 20, 2015

Color Diagnostics, LLC DBA Color Health

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Breast-ovarian cancer, familial, susceptibility to, 4

Benign:1

Jan 09, 2018

Counsyl

Significance:Likely benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

This submission and the accompanying classification are no longer maintained by the submitter. For more information on current observations and classification, please contact variantquestions@myriad.com. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.85

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.080

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over