rs709167

Variant names:

• chr3-12461456-G-T
• rs709167

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 0.578 in 151,996 control chromosomes in the GnomAD database, including 26,671 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 0.58 (26671 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.721 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: 0.578 AC: 87818 AN: 151878 Hom.: 26628 Cov.: 32

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.578 AC: 87912 AN: 151996 Hom.: 26671 Cov.: 32 AF XY: 0.574 AC XY: 42637 AN XY: 74270

African (AFR) AF: 0.728 AC: 30161 AN: 41448

American (AMR) AF: 0.614 AC: 9383 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2010 AN: 3466

East Asian (EAS) AF: 0.137 AC: 708 AN: 5180

South Asian (SAS) AF: 0.293 AC: 1412 AN: 4818

European-Finnish (FIN) AF: 0.546 AC: 5760 AN: 10550

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.539 AC: 36636 AN: 67952

Other (OTH) AF: 0.577 AC: 1215 AN: 2104

Alfa AF: 0.578 Hom.: 9129

Bravo AF: 0.592

Asia WGS AF: 0.361 AC: 1259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	6.0
DANN	Benign	0.65
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs709167; hg19: chr3-12502955;