dbSNP rs11683503: ENSG00000286260:n.103+23015A>G (chr2-78971042-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000776871.1(ENSG00000286260):n.103+23015A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,082 control chromosomes in the GnomAD database, including 3,240 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 0.17 ( 3240 hom., cov: 32)

Consequence

ENSG00000286260
ENST00000776871.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.23

Publications

3 publications found

Variant links:

Genes affected

ENSG00000286260 (HGNC:):

ENSG00000286260 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=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.351 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
ENSG00000286260	ENST00000776871.1 link	n.103+23015A>G		intron_variant	Intron 1 of 3
ENSG00000286260	ENST00000776872.1 link	n.62+23015A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.167

AC:

25369

AN:

151964

Hom.:

3231

Cov.:

show subpopulations

Gnomad AFR

AF:

0.356

Gnomad AMI

AF:

0.0857

Gnomad AMR

AF:

0.130

Gnomad ASJ

AF:

0.0700

Gnomad EAS

AF:

0.123

Gnomad SAS

AF:

0.169

Gnomad FIN

AF:

0.0849

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.0835

Gnomad OTH

AF:

0.143

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

GnomAD4 genome

AF:

0.167

AC:

25429

AN:

152082

Hom.:

3240

Cov.:

AF XY:

0.167

AC XY:

12386

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.356

AC:

14751

AN:

41428

American (AMR)

AF:

0.130

AC:

1985

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.0700

AC:

243

AN:

3472

East Asian (EAS)

AF:

0.123

AC:

634

AN:

5174

South Asian (SAS)

AF:

0.169

AC:

813

AN:

4822

European-Finnish (FIN)

AF:

0.0849

AC:

899

AN:

10590

Middle Eastern (MID)

AF:

0.116

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0835

AC:

5680

AN:

68006

Other (OTH)

AF:

0.147

AC:

312

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

980

1959

2939

3918

4898

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

266

532

798

1064

1330

<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:

0.113

Hom.:

4540

Bravo

AF:

0.176

Asia WGS

AF:

0.173

AC:

600

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.2

(source)

DANN

Benign

0.56

PhyloP100

-1.2

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