3-191647345-C-T

Variant names:

• chr3-191647345-C-T
• rs9843456

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 0.381 in 151,956 control chromosomes in the GnomAD database, including 13,158 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 0.38 (13158 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.984
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.64 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: 0.381 AC: 57779 AN: 151838 Hom.: 13115 Cov.: 32

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.381 AC: 57881 AN: 151956 Hom.: 13158 Cov.: 32 AF XY: 0.380 AC XY: 28189 AN XY: 74242

African (AFR) AF: 0.647 AC: 26821 AN: 41474

American (AMR) AF: 0.343 AC: 5235 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1016 AN: 3470

East Asian (EAS) AF: 0.390 AC: 2015 AN: 5168

South Asian (SAS) AF: 0.350 AC: 1685 AN: 4816

European-Finnish (FIN) AF: 0.251 AC: 2643 AN: 10524

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17602 AN: 67918

Other (OTH) AF: 0.333 AC: 703 AN: 2110

Alfa AF: 0.291 Hom.: 9571

Bravo AF: 0.397

Asia WGS AF: 0.376 AC: 1310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.37
DANN	Benign	0.73
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs9843456; hg19: chr3-191365134;