4-124494379-C-T

Variant names:

• chr4-124494379-C-T
• rs6534441

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 0.592 in 152,020 control chromosomes in the GnomAD database, including 28,479 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 0.59 (28479 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.34
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 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: 0.593 AC: 90006 AN: 151904 Hom.: 28465 Cov.: 32

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.592 AC: 90060 AN: 152020 Hom.: 28479 Cov.: 32 AF XY: 0.596 AC XY: 44250 AN XY: 74306

African (AFR) AF: 0.356 AC: 14774 AN: 41444

American (AMR) AF: 0.731 AC: 11178 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.625 AC: 2171 AN: 3472

East Asian (EAS) AF: 0.754 AC: 3898 AN: 5172

South Asian (SAS) AF: 0.746 AC: 3596 AN: 4822

European-Finnish (FIN) AF: 0.614 AC: 6472 AN: 10548

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

European-Non Finnish (NFE) AF: 0.673 AC: 45742 AN: 67966

Other (OTH) AF: 0.632 AC: 1333 AN: 2108

Alfa AF: 0.639 Hom.: 59236

Bravo AF: 0.592

Asia WGS AF: 0.731 AC: 2542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.17
DANN	Benign	0.39
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs6534441; hg19: chr4-125415534;