dbSNP rs7042508: ENSG00000308694:n.185+18662G>C (chr9-38746454-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000835853.1(ENSG00000308694):n.185+18662G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0958 in 152,026 control chromosomes in the GnomAD database, including 1,023 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 0.096 ( 1023 hom., cov: 33)

Consequence

ENSG00000308694
ENST00000835853.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.105

Publications

2 publications found

Variant links:

Genes affected

ENSG00000308694 (HGNC:):

ENSG00000308694 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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000308694	ENST00000835853.1 link	n.185+18662G>C	intron_variant	Intron 1 of 1
ENSG00000308694	ENST00000835854.1 link	n.376+8246G>C	intron_variant	Intron 3 of 4
ENSG00000308694	ENST00000835855.1 link	n.72+18662G>C	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0957

AC:

14542

AN:

151906

Hom.:

1019

Cov.:

show subpopulations

Gnomad AFR

AF:

0.191

Gnomad AMI

AF:

0.0164

Gnomad AMR

AF:

0.0561

Gnomad ASJ

AF:

0.0813

Gnomad EAS

AF:

0.102

Gnomad SAS

AF:

0.0236

Gnomad FIN

AF:

0.0422

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.0622

Gnomad OTH

AF:

0.0815

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

GnomAD4 genome

AF:

0.0958

AC:

14568

AN:

152026

Hom.:

1023

Cov.:

AF XY:

0.0926

AC XY:

6884

AN XY:

74340

show subpopulations

African (AFR)

AF:

0.191

AC:

7893

AN:

41300

American (AMR)

AF:

0.0560

AC:

857

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.0813

AC:

282

AN:

3470

East Asian (EAS)

AF:

0.102

AC:

529

AN:

5180

South Asian (SAS)

AF:

0.0240

AC:

116

AN:

4824

European-Finnish (FIN)

AF:

0.0422

AC:

448

AN:

10616

Middle Eastern (MID)

AF:

0.0918

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0622

AC:

4233

AN:

68022

Other (OTH)

AF:

0.0797

AC:

168

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

656

1312

1967

2623

3279

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

148

296

444

592

740

<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:

0.0768

Hom.:

Bravo

AF:

0.104

Asia WGS

AF:

0.0560

AC:

194

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.0

(source)

DANN

Benign

0.71

PhyloP100

-0.10

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