dbSNP rs4131931: :null (chr8-67846739-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.841 in 152,206 control chromosomes in the GnomAD database, including 53,989 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 0.84 ( 53989 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.598

Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.01).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.885 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

Frequencies

GnomAD3 genomes

AF:

0.841

AC:

127951

AN:

152088

Hom.:

53965

Cov.:

show subpopulations

Gnomad AFR

AF:

0.832

Gnomad AMI

AF:

0.851

Gnomad AMR

AF:

0.898

Gnomad ASJ

AF:

0.844

Gnomad EAS

AF:

0.795

Gnomad SAS

AF:

0.846

Gnomad FIN

AF:

0.899

Gnomad MID

AF:

0.832

Gnomad NFE

AF:

0.828

Gnomad OTH

AF:

0.841

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

GnomAD4 genome

AF:

0.841

AC:

128028

AN:

152206

Hom.:

53989

Cov.:

AF XY:

0.843

AC XY:

62777

AN XY:

74428

show subpopulations

Gnomad4 AFR

AF:

0.832

Gnomad4 AMR

AF:

0.898

Gnomad4 ASJ

AF:

0.844

Gnomad4 EAS

AF:

0.794

Gnomad4 SAS

AF:

0.846

Gnomad4 FIN

AF:

0.899

Gnomad4 NFE

AF:

0.828

Gnomad4 OTH

AF:

0.838

Alfa

AF:

0.835

Hom.:

8968

Bravo

AF:

0.840

Asia WGS

AF:

0.793

AC:

2757

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

1.3

DANN

Benign

0.59

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over