dbSNP rs2505999: ENSG00000303432:n.51+1062G>A (chr10-43075999-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000794440.1(ENSG00000303432):n.51+1062G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 152,104 control chromosomes in the GnomAD database, including 9,591 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 0.35 ( 9591 hom., cov: 33)

Consequence

ENSG00000303432
ENST00000794440.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.662

Publications

7 publications found

Variant links:

Genes affected

ENSG00000303432 (HGNC:):

ENSG00000303432 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=-0.82).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000303432	ENST00000794440.1 link	n.51+1062G>A	intron_variant	Intron 1 of 2
ENSG00000303432	ENST00000794441.1 link	n.116+1034G>A	intron_variant	Intron 1 of 3
ENSG00000303432	ENST00000794442.1 link	n.107+1034G>A	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.347

AC:

52752

AN:

151986

Hom.:

9569

Cov.:

show subpopulations

Gnomad AFR

AF:

0.244

Gnomad AMI

AF:

0.482

Gnomad AMR

AF:

0.405

Gnomad ASJ

AF:

0.328

Gnomad EAS

AF:

0.316

Gnomad SAS

AF:

0.415

Gnomad FIN

AF:

0.362

Gnomad MID

AF:

0.377

Gnomad NFE

AF:

0.391

Gnomad OTH

AF:

0.353

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

GnomAD4 genome

AF:

0.347

AC:

52799

AN:

152104

Hom.:

9591

Cov.:

AF XY:

0.349

AC XY:

25925

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.244

AC:

10138

AN:

41504

American (AMR)

AF:

0.405

AC:

6202

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.328

AC:

1140

AN:

3472

East Asian (EAS)

AF:

0.316

AC:

1634

AN:

5174

South Asian (SAS)

AF:

0.415

AC:

1999

AN:

4814

European-Finnish (FIN)

AF:

0.362

AC:

3829

AN:

10574

Middle Eastern (MID)

AF:

0.391

AC:

115

AN:

294

European-Non Finnish (NFE)

AF:

0.391

AC:

26554

AN:

67954

Other (OTH)

AF:

0.355

AC:

750

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

1724

3447

5171

6894

8618

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

524

1048

1572

2096

2620

<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:

0.378

Hom.:

23716

Bravo

AF:

0.346

Asia WGS

AF:

0.355

AC:

1234

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

2.4

(source)

DANN

Benign

0.71

PhyloP100

-0.66

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