dbSNP rs6743931: ENSG00000286525:n.318-32660G>A (chr2-239496966-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 ENST00000659636.1(ENSG00000286525):n.318-32660G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 150,812 control chromosomes in the GnomAD database, including 2,207 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 0.16 ( 2207 hom., cov: 33)

Consequence

ENSG00000286525
ENST00000659636.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.318

Publications

9 publications found

Variant links:

Genes affected

ENSG00000286525 (HGNC:):

ENSG00000286525 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 (AFR) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000286525	ENST00000659636.1 link	n.318-32660G>A	intron_variant	Intron 1 of 1
ENSG00000288082	ENST00000776286.1 link	n.175-530C>T	intron_variant	Intron 1 of 1
ENSG00000288082	ENST00000776287.1 link	n.69-530C>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.165

AC:

24833

AN:

150692

Hom.:

2207

Cov.:

show subpopulations

Gnomad AFR

AF:

0.221

Gnomad AMI

AF:

0.159

Gnomad AMR

AF:

0.102

Gnomad ASJ

AF:

0.116

Gnomad EAS

AF:

0.00743

Gnomad SAS

AF:

0.146

Gnomad FIN

AF:

0.182

Gnomad MID

AF:

0.133

Gnomad NFE

AF:

0.159

Gnomad OTH

AF:

0.160

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

GnomAD4 genome

AF:

0.165

AC:

24847

AN:

150812

Hom.:

2207

Cov.:

AF XY:

0.162

AC XY:

11912

AN XY:

73562

show subpopulations

African (AFR)

AF:

0.221

AC:

9032

AN:

40954

American (AMR)

AF:

0.101

AC:

1533

AN:

15124

Ashkenazi Jewish (ASJ)

AF:

0.116

AC:

404

AN:

3468

East Asian (EAS)

AF:

0.00745

AC:

AN:

5102

South Asian (SAS)

AF:

0.146

AC:

697

AN:

4790

European-Finnish (FIN)

AF:

0.182

AC:

1872

AN:

10272

Middle Eastern (MID)

AF:

0.135

AC:

AN:

288

European-Non Finnish (NFE)

AF:

0.159

AC:

10755

AN:

67812

Other (OTH)

AF:

0.159

AC:

333

AN:

2096

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1024

2048

3072

4096

5120

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

260

520

780

1040

1300

<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:

0.154

Hom.:

9099

Bravo

AF:

0.160

Asia WGS

AF:

0.0870

AC:

303

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

4.4

(source)

DANN

Benign

0.62

PhyloP100

-0.32

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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