6-43769749-C-T

Variant names:

• chr6-43769749-C-T
• rs833061

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 0.559 in 151,884 control chromosomes in the GnomAD database, including 24,103 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 0.56 (24103 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265
• Publications: 548 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84807 AN: 151766 Hom.: 24081 Cov.: 31

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.559 AC: 84887 AN: 151884 Hom.: 24103 Cov.: 31 AF XY: 0.557 AC XY: 41324 AN XY: 74228

African (AFR) AF: 0.659 AC: 27325 AN: 41450

American (AMR) AF: 0.590 AC: 9007 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1858 AN: 3472

East Asian (EAS) AF: 0.726 AC: 3722 AN: 5130

South Asian (SAS) AF: 0.552 AC: 2654 AN: 4806

European-Finnish (FIN) AF: 0.448 AC: 4713 AN: 10524

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 33973 AN: 67920

Other (OTH) AF: 0.583 AC: 1231 AN: 2112

Alfa AF: 0.532 Hom.: 38625

Bravo AF: 0.578

Asia WGS AF: 0.606 AC: 2104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	11
DANN	Benign	0.93
PhyloP100		-0.27
PromoterAI		-0.022	Neutral

Splicing

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

Other links and lift over

dbSNP: rs833061; hg19: chr6-43737486;