dbSNP rs13409979: ENSG00000287621:n.366-3849G>A (chr2-183489082-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 ENST00000653710.1(ENSG00000287621):n.366-3849G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 151,894 control chromosomes in the GnomAD database, including 1,533 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 0.14 ( 1533 hom., cov: 32)

Consequence

ENSG00000287621
ENST00000653710.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0110

Publications

1 publications found

Variant links:

Genes affected

ENSG00000287621 (HGNC:):

ENSG00000287621 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=-0.91).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000287621	ENST00000653710.1 link	n.366-3849G>A	intron_variant	Intron 3 of 3
ENSG00000287621	ENST00000804704.1 link	n.210-35986G>A	intron_variant	Intron 2 of 2
ENSG00000287621	ENST00000804705.1 link	n.282-35986G>A	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.136

AC:

20714

AN:

151776

Hom.:

1535

Cov.:

show subpopulations

Gnomad AFR

AF:

0.179

Gnomad AMI

AF:

0.0727

Gnomad AMR

AF:

0.133

Gnomad ASJ

AF:

0.120

Gnomad EAS

AF:

0.0611

Gnomad SAS

AF:

0.219

Gnomad FIN

AF:

0.0542

Gnomad MID

AF:

0.223

Gnomad NFE

AF:

0.125

Gnomad OTH

AF:

0.145

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

GnomAD4 genome

AF:

0.136

AC:

20714

AN:

151894

Hom.:

1533

Cov.:

AF XY:

0.134

AC XY:

9985

AN XY:

74244

show subpopulations

African (AFR)

AF:

0.179

AC:

7389

AN:

41380

American (AMR)

AF:

0.132

AC:

2020

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.120

AC:

415

AN:

3468

East Asian (EAS)

AF:

0.0613

AC:

317

AN:

5172

South Asian (SAS)

AF:

0.219

AC:

1055

AN:

4810

European-Finnish (FIN)

AF:

0.0542

AC:

572

AN:

10552

Middle Eastern (MID)

AF:

0.219

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.125

AC:

8514

AN:

67948

Other (OTH)

AF:

0.143

AC:

302

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

916

1832

2748

3664

4580

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

238

476

714

952

1190

<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:

0.127

Hom.:

4461

Bravo

AF:

0.141

Asia WGS

AF:

0.143

AC:

499

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

4.1

(source)

DANN

Benign

0.71

PhyloP100

0.011

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