rs709167

chr3-12461456-G-T

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 0.578 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.728

Gnomad4 AMR AF: 0.614

Gnomad4 ASJ AF: 0.580

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.546

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.577

Alfa AF: 0.577 Hom.: 7198

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs709167; hg19: chr3-12502955;