dbSNP rs1860188: ENSG00000301139:n.238+336G>A (chr17-34251537-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 ENST00000776537.1(ENSG00000301139):n.238+336G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,192 control chromosomes in the GnomAD database, including 1,787 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 0.15 ( 1787 hom., cov: 32)

Consequence

ENSG00000301139
ENST00000776537.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.274

Publications

5 publications found

Variant links:

Genes affected

ENSG00000301139 (HGNC:):

ENSG00000301139 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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000301139	ENST00000776537.1 link	n.238+336G>A	intron_variant	Intron 2 of 2
ENSG00000301139	ENST00000776538.1 link	n.238+336G>A	intron_variant	Intron 2 of 2
ENSG00000301139	ENST00000776539.1 link	n.236+336G>A	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.149

AC:

22679

AN:

152074

Hom.:

1787

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0890

Gnomad AMI

AF:

0.0954

Gnomad AMR

AF:

0.145

Gnomad ASJ

AF:

0.240

Gnomad EAS

AF:

0.184

Gnomad SAS

AF:

0.162

Gnomad FIN

AF:

0.164

Gnomad MID

AF:

0.168

Gnomad NFE

AF:

0.176

Gnomad OTH

AF:

0.166

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

GnomAD4 genome

AF:

0.149

AC:

22670

AN:

152192

Hom.:

1787

Cov.:

AF XY:

0.149

AC XY:

11104

AN XY:

74386

show subpopulations

African (AFR)

AF:

0.0889

AC:

3692

AN:

41518

American (AMR)

AF:

0.145

AC:

2220

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.240

AC:

833

AN:

3468

East Asian (EAS)

AF:

0.183

AC:

949

AN:

5176

South Asian (SAS)

AF:

0.161

AC:

776

AN:

4828

European-Finnish (FIN)

AF:

0.164

AC:

1740

AN:

10584

Middle Eastern (MID)

AF:

0.177

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.176

AC:

11975

AN:

68004

Other (OTH)

AF:

0.164

AC:

346

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1004

2007

3011

4014

5018

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

254

508

762

1016

1270

<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:

0.163

Hom.:

552

Bravo

AF:

0.145

Asia WGS

AF:

0.167

AC:

583

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

3.3

(source)

DANN

Benign

0.39

PhyloP100

0.27

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