4-40379193-T-C

Variant names:

• chr4-40379193-T-C
• rs6447650

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 0.911 in 152,256 control chromosomes in the GnomAD database, including 63,319 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 0.91 (63319 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.911 AC: 138530 AN: 152138 Hom.: 63273 Cov.: 31

Gnomad AFR AF: 0.947

Gnomad AMI AF: 0.921

Gnomad AMR AF: 0.802

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.958

Gnomad FIN AF: 0.954

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.898

Gnomad OTH AF: 0.888

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

GnomAD4 genome AF: 0.911 AC: 138633 AN: 152256 Hom.: 63319 Cov.: 31 AF XY: 0.911 AC XY: 67842 AN XY: 74444

African (AFR) AF: 0.947 AC: 39328 AN: 41538

American (AMR) AF: 0.802 AC: 12274 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.875 AC: 3038 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5169 AN: 5176

South Asian (SAS) AF: 0.958 AC: 4621 AN: 4826

European-Finnish (FIN) AF: 0.954 AC: 10113 AN: 10604

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.898 AC: 61109 AN: 68022

Other (OTH) AF: 0.889 AC: 1880 AN: 2114

Alfa AF: 0.904 Hom.: 20583

Bravo AF: 0.901

Asia WGS AF: 0.972 AC: 3381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.30
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs6447650; hg19: chr4-40381210;