rs709086

Variant names:

• chr3-191738431-T-C
• rs709086

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 0.222 in 152,104 control chromosomes in the GnomAD database, including 4,292 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 0.22 (4292 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.302 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: 0.222 AC: 33754 AN: 151986 Hom.: 4285 Cov.: 32

Gnomad AFR AF: 0.0866

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.222 AC: 33772 AN: 152104 Hom.: 4292 Cov.: 32 AF XY: 0.228 AC XY: 16916 AN XY: 74326

Gnomad4 AFR AF: 0.0864

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.223

Alfa AF: 0.264 Hom.: 11266

Bravo AF: 0.212

Asia WGS AF: 0.324 AC: 1124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.4
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs709086; hg19: chr3-191456220;