rs6791663

Variant names:

• chr3-182251564-G-A
• rs6791663

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 0.205 in 151,754 control chromosomes in the GnomAD database, including 3,728 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 0.20 (3728 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.686

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.353 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: 0.205 AC: 31065 AN: 151636 Hom.: 3716 Cov.: 31

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.0800

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.205 AC: 31103 AN: 151754 Hom.: 3728 Cov.: 31 AF XY: 0.201 AC XY: 14883 AN XY: 74166

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.0800

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.208

Alfa AF: 0.173 Hom.: 1274

Bravo AF: 0.214

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.75
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6791663; hg19: chr3-181969352;