4-79897263-T-C

Variant names:

• chr4-79897263-T-C
• rs11939401

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 0.809 in 151,866 control chromosomes in the GnomAD database, including 49,984 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 0.81 (49984 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.420
• Publications: 4 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 (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.809 AC: 122816 AN: 151748 Hom.: 49927 Cov.: 29

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.786

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.828

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.902

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.809 AC: 122935 AN: 151866 Hom.: 49984 Cov.: 29 AF XY: 0.812 AC XY: 60202 AN XY: 74182

African (AFR) AF: 0.795 AC: 32923 AN: 41424

American (AMR) AF: 0.860 AC: 13082 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.828 AC: 2873 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5136 AN: 5138

South Asian (SAS) AF: 0.902 AC: 4331 AN: 4802

European-Finnish (FIN) AF: 0.758 AC: 7995 AN: 10554

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.794 AC: 53960 AN: 67940

Other (OTH) AF: 0.801 AC: 1694 AN: 2114

Alfa AF: 0.803 Hom.: 152732

Bravo AF: 0.814

Asia WGS AF: 0.934 AC: 3246 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	0.039
DANN	Benign	0.49
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs11939401; hg19: chr4-80818417;