4-40301616-G-T

Variant names:

• chr4-40301616-G-T
• rs6832151

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.718 in 152,124 control chromosomes in the GnomAD database, including 39,219 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 0.72 (39219 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82
• Publications: 38 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109098 AN: 152006 Hom.: 39198 Cov.: 32

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.898

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.644

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.755

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.718 AC: 109173 AN: 152124 Hom.: 39219 Cov.: 32 AF XY: 0.720 AC XY: 53559 AN XY: 74362

African (AFR) AF: 0.693 AC: 28758 AN: 41474

American (AMR) AF: 0.734 AC: 11225 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.710 AC: 2466 AN: 3472

East Asian (EAS) AF: 0.645 AC: 3337 AN: 5174

South Asian (SAS) AF: 0.778 AC: 3757 AN: 4826

European-Finnish (FIN) AF: 0.755 AC: 7988 AN: 10578

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.722 AC: 49084 AN: 67990

Other (OTH) AF: 0.721 AC: 1522 AN: 2110

Alfa AF: 0.719 Hom.: 176211

Bravo AF: 0.715

Asia WGS AF: 0.689 AC: 2397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.043
DANN	Benign	0.36
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs6832151; hg19: chr4-40303633;