rs709086

Positions:

• chr3-191738431-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;