dbSNP rs763931520: ANKRD30A:p.Glu1314ThrfsTer28 (chr10-37219650-CTG-C) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_052997.3(ANKRD30A):c.3939_3940delTG(p.Glu1314ThrfsTer28) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00429 in 1,609,780 control chromosomes in the GnomAD database, including 25 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.0030 ( 2 hom., cov: 30)

Exomes 𝑓: 0.0044 ( 23 hom. )

Consequence

ANKRD30A
NM_052997.3 frameshift

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, single submitter U:2

Conservation

PhyloP100: 2.06

Variant links:

Genes affected

ANKRD30A (HGNC:17234): (ankyrin repeat domain 30A) This gene encodes a DNA-binding transcription factor that is uniquely expressed in mammary epithelium and the testis. Altered expression levels have been associated with breast cancer progression. [provided by RefSeq, Nov 2016]

ANKRD30A links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD30A	NM_052997.3 link	c.3939_3940delTG	p.Glu1314ThrfsTer28	frameshift_variant	Exon 34 of 36	ENST00000361713.2	NP_443723.3	Q9BXX3R4GNA2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
ANKRD30A	ENST00000361713.2 link	c.3939_3940delTG	p.Glu1314ThrfsTer28	frameshift_variant	Exon 34 of 36	5	NM_052997.3	ENSP00000354432.2	Q9BXX3R4GNA2
ANKRD30A	ENST00000374660.7 link	c.4296_4297delTG	p.Glu1433ThrfsTer28	frameshift_variant	Exon 40 of 42	5		ENSP00000363792.2	Q5W026
ANKRD30A	ENST00000602533.7 link	c.3939_3940delTG	p.Glu1314ThrfsTer28	frameshift_variant	Exon 34 of 36	5		ENSP00000473551.2	Q9BXX3
ANKRD30A	ENST00000696674.1 link	c.672_673delTG	p.Glu225ThrfsTer28	frameshift_variant	Exon 1 of 2			ENSP00000512798.1	A0A8Q3WLF6

Frequencies

GnomAD3 genomes

AF:

0.00304

AC:

459

AN:

150902

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000849

Gnomad AMI

AF:

0.0340

Gnomad AMR

AF:

0.000997

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00604

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00466

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.00264

AC:

653

AN:

247458

AF XY:

0.00270

show subpopulations

Gnomad AFR exome

AF:

0.000587

Gnomad AMR exome

AF:

0.000671

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00377

Gnomad NFE exome

AF:

0.00470

Gnomad OTH exome

AF:

0.00217

GnomAD4 exome

AF:

0.00442

AC:

6444

AN:

1458878

Hom.:

AF XY:

0.00421

AC XY:

3058

AN XY:

725754

show subpopulations

Gnomad4 AFR exome

AF:

0.000691

AC:

AN:

33302

Gnomad4 AMR exome

AF:

0.000719

AC:

AN:

44510

Gnomad4 ASJ exome

AF:

0.00

AC:

AN:

25986

Gnomad4 EAS exome

AF:

0.00

AC:

AN:

39534

Gnomad4 SAS exome

AF:

0.0000116

AC:

AN:

86114

Gnomad4 FIN exome

AF:

0.00405

AC:

216

AN:

53348

Gnomad4 NFE exome

AF:

0.00524

AC:

5818

AN:

1110154

Gnomad4 Remaining exome

AF:

0.00583

AC:

351

AN:

60188

Heterozygous variant carriers

372

743

1115

1486

1858

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

226

452

678

904

1130

<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:

0.00304

AC:

459

AN:

150902

Hom.:

Cov.:

AF XY:

0.00305

AC XY:

225

AN XY:

73678

show subpopulations

Gnomad4 AFR

AF:

0.000849

AC:

0.000848938

AN:

0.000848938

Gnomad4 AMR

AF:

0.000997

AC:

0.00099681

AN:

0.00099681

Gnomad4 ASJ

AF:

0.00

AC:

AN:

Gnomad4 EAS

AF:

0.00

AC:

AN:

Gnomad4 SAS

AF:

0.00

AC:

AN:

Gnomad4 FIN

AF:

0.00604

AC:

0.00604344

AN:

0.00604344

Gnomad4 NFE

AF:

0.00466

AC:

0.0046629

AN:

0.0046629

Gnomad4 OTH

AF:

0.00

AC:

AN:

Heterozygous variant carriers

113

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

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:

0.00261

Hom.:

Bravo

AF:

0.00261

EpiCase

AF:

0.00415

EpiControl

AF:

0.00392

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:2

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Uncertain:1

Breakthrough Genomics, Breakthrough Genomics

Significance:Uncertain significance

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Familial cancer of breast

Uncertain:1

Feb 01, 2014

Faculty of Pharmacy, Medical University of Gdansk

Significance:Uncertain significance

Review Status:no assertion criteria provided

Collection Method:research

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Mutation Taster

=189/11

disease causing (fs/PTC)

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