Variant 17-35100823-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_002878.4(RAD51D):c.*130A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00744 in 785,936 control chromosomes in the GnomAD database, including 177 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0057 ( 34 hom., cov: 32)

Exomes 𝑓: 0.0079 ( 143 hom. )

Consequence

RAD51D
NM_002878.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.536

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 links:

RAD51L3-RFFL (HGNC:):

RAD51L3-RFFL links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 17-35100823-T-G is Benign according to our data. Variant chr17-35100823-T-G is described in ClinVar as [Benign]. Clinvar id is 1276573.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0924 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RAD51D	NM_002878.4 linkuse as main transcript	c.*130A>C		3_prime_UTR_variant	10/10	ENST00000345365.11	NP_002869.3
RAD51L3-RFFL	NR_037714.1 linkuse as main transcript	n.655+378A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RAD51D	ENST00000345365.11 linkuse as main transcript	c.*130A>C		3_prime_UTR_variant	10/10	1	NM_002878.4	ENSP00000338790	P1	O75771-1

Frequencies

GnomAD3 genomes

AF:

0.00568

AC:

865

AN:

152222

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000289

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00825

Gnomad ASJ

AF:

0.00634

Gnomad EAS

AF:

0.0995

Gnomad SAS

AF:

0.00641

Gnomad FIN

AF:

0.00649

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00113

Gnomad OTH

AF:

0.00526

GnomAD3 exomes

AF:

0.0121

AC:

2209

AN:

182224

Hom.:

AF XY:

0.0113

AC XY:

1108

AN XY:

97808

show subpopulations

Gnomad AFR exome

AF:

0.000285

Gnomad AMR exome

AF:

0.0178

Gnomad ASJ exome

AF:

0.00403

Gnomad EAS exome

AF:

0.104

Gnomad SAS exome

AF:

0.00335

Gnomad FIN exome

AF:

0.00814

Gnomad NFE exome

AF:

0.00124

Gnomad OTH exome

AF:

0.00783

GnomAD4 exome

AF:

0.00787

AC:

4987

AN:

633596

Hom.:

143

Cov.:

AF XY:

0.00754

AC XY:

2569

AN XY:

340650

show subpopulations

Gnomad4 AFR exome

AF:

0.000173

Gnomad4 AMR exome

AF:

0.0152

Gnomad4 ASJ exome

AF:

0.00424

Gnomad4 EAS exome

AF:

0.0884

Gnomad4 SAS exome

AF:

0.00393

Gnomad4 FIN exome

AF:

0.00799

Gnomad4 NFE exome

AF:

0.00139

Gnomad4 OTH exome

AF:

0.00586

GnomAD4 genome

AF:

0.00566

AC:

863

AN:

152340

Hom.:

Cov.:

AF XY:

0.00659

AC XY:

491

AN XY:

74502

show subpopulations

Gnomad4 AFR

AF:

0.000289

Gnomad4 AMR

AF:

0.00824

Gnomad4 ASJ

AF:

0.00634

Gnomad4 EAS

AF:

0.0995

Gnomad4 SAS

AF:

0.00642

Gnomad4 FIN

AF:

0.00649

Gnomad4 NFE

AF:

0.00113

Gnomad4 OTH

AF:

0.00473

Alfa

AF:

0.00178

Hom.:

Bravo

AF:

0.00708

Asia WGS

AF:

0.0450

AC:

155

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 21, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

4.8

DANN

Benign

0.75

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over