dbSNP rs10508112: ENSG00000302562:n.427-3801G>A (chr13-103528870-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000787871.1(ENSG00000302562):n.427-3801G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0532 in 151,988 control chromosomes in the GnomAD database, including 342 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.053 ( 342 hom., cov: 32)

Consequence

ENSG00000302562
ENST00000787871.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.782

Publications

0 publications found

Variant links:

Genes affected

ENSG00000302562 (HGNC:):

ENSG00000302562 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302562	ENST00000787871.1 link	n.427-3801G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0531

AC:

8063

AN:

151870

Hom.:

342

Cov.:

show subpopulations

Gnomad AFR

AF:

0.108

Gnomad AMI

AF:

0.00987

Gnomad AMR

AF:

0.0379

Gnomad ASJ

AF:

0.0294

Gnomad EAS

AF:

0.00716

Gnomad SAS

AF:

0.0278

Gnomad FIN

AF:

0.0220

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0349

Gnomad OTH

AF:

0.0489

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0532

AC:

8079

AN:

151988

Hom.:

342

Cov.:

AF XY:

0.0517

AC XY:

3844

AN XY:

74284

show subpopulations

African (AFR)

AF:

0.108

AC:

4495

AN:

41486

American (AMR)

AF:

0.0378

AC:

576

AN:

15228

Ashkenazi Jewish (ASJ)

AF:

0.0294

AC:

102

AN:

3464

East Asian (EAS)

AF:

0.00698

AC:

AN:

5156

South Asian (SAS)

AF:

0.0276

AC:

133

AN:

4818

European-Finnish (FIN)

AF:

0.0220

AC:

233

AN:

10584

Middle Eastern (MID)

AF:

0.0408

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0349

AC:

2373

AN:

67936

Other (OTH)

AF:

0.0521

AC:

110

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

389

778

1166

1555

1944

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

164

246

328

410

<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:

0.0507

Hom.:

Bravo

AF:

0.0568

Asia WGS

AF:

0.0380

AC:

132

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.41

(source)

DANN

Benign

0.60

PhyloP100

-0.78

Splicing

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over