Variant 10-37219650-CTG-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_052997.3(ANKRD30A):c.3939_3940del(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:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ANKRD30A	NM_052997.3 linkuse as main transcript	c.3939_3940del	p.Glu1314ThrfsTer28	frameshift_variant	34/36	ENST00000361713.2	NP_443723.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
ANKRD30A	ENST00000361713.2 linkuse as main transcript	c.3939_3940del	p.Glu1314ThrfsTer28	frameshift_variant	34/36	5	NM_052997.3	ENSP00000354432	A2
ANKRD30A	ENST00000374660.7 linkuse as main transcript	c.4296_4297del	p.Glu1433ThrfsTer28	frameshift_variant	40/42	5		ENSP00000363792	P4
ANKRD30A	ENST00000602533.7 linkuse as main transcript	c.3939_3940del	p.Glu1314ThrfsTer28	frameshift_variant	34/36	5		ENSP00000473551	A2
ANKRD30A	ENST00000696674.1 linkuse as main transcript	c.672_673del	p.Glu225ThrfsTer28	frameshift_variant	1/2			ENSP00000512798

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

GnomAD3 exomes

AF:

0.00264

AC:

653

AN:

247458

Hom.:

AF XY:

0.00270

AC XY:

362

AN XY:

134322

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 SAS 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

Gnomad4 AMR exome

AF:

0.000719

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000116

Gnomad4 FIN exome

AF:

0.00405

Gnomad4 NFE exome

AF:

0.00524

Gnomad4 OTH exome

AF:

0.00583

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

Gnomad4 AMR

AF:

0.000997

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00604

Gnomad4 NFE

AF:

0.00466

Gnomad4 OTH

AF:

0.00

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

Uncertain significance, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Familial cancer of breast

Uncertain:1

Uncertain significance, no assertion criteria provided

research

Faculty of Pharmacy, Medical University of Gdansk

Feb 01, 2014

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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