rs6762743

Variant names:

• chr3-179294212-C-T
• rs6762743

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.324

Alfa AF: 0.284 Hom.: 2965

Bravo AF: 0.305

Asia WGS AF: 0.269 AC: 935 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6762743; hg19: chr3-179012000;