rs6762743

Variant names:

• chr3-179294212-C-T
• rs6762743

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 0.289 in 151,968 control chromosomes in the GnomAD database, including 6,613 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 0.29 (6613 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.331 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: 0.290 AC: 43969 AN: 151850 Hom.: 6614 Cov.: 33

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.289 AC: 43971 AN: 151968 Hom.: 6613 Cov.: 33 AF XY: 0.287 AC XY: 21336 AN XY: 74306

African (AFR) AF: 0.336 AC: 13903 AN: 41416

American (AMR) AF: 0.296 AC: 4515 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1352 AN: 3472

East Asian (EAS) AF: 0.196 AC: 1014 AN: 5174

South Asian (SAS) AF: 0.333 AC: 1609 AN: 4826

European-Finnish (FIN) AF: 0.183 AC: 1928 AN: 10552

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18444 AN: 67950

Other (OTH) AF: 0.324 AC: 684 AN: 2110

Alfa AF: 0.285 Hom.: 3336

Bravo AF: 0.305

Asia WGS AF: 0.269 AC: 935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.84
DANN	Benign	0.76
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs6762743; hg19: chr3-179012000;