rs3117292

Variant names:

• chr6-29684422-A-G
• rs3117292

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 0.425 in 152,080 control chromosomes in the GnomAD database, including 14,527 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 0.42 (14527 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 25 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.557 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: 0.424 AC: 64501 AN: 151962 Hom.: 14514 Cov.: 32

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.425 AC: 64559 AN: 152080 Hom.: 14527 Cov.: 32 AF XY: 0.420 AC XY: 31219 AN XY: 74340

African (AFR) AF: 0.563 AC: 23353 AN: 41462

American (AMR) AF: 0.471 AC: 7193 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1745 AN: 3468

East Asian (EAS) AF: 0.249 AC: 1290 AN: 5182

South Asian (SAS) AF: 0.368 AC: 1776 AN: 4824

European-Finnish (FIN) AF: 0.246 AC: 2603 AN: 10576

Middle Eastern (MID) AF: 0.490 AC: 143 AN: 292

European-Non Finnish (NFE) AF: 0.371 AC: 25204 AN: 67976

Other (OTH) AF: 0.464 AC: 979 AN: 2112

Alfa AF: 0.391 Hom.: 39665

Bravo AF: 0.451

Asia WGS AF: 0.276 AC: 961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.40
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs3117292; hg19: chr6-29652199;