chr3-94491352-A-G

Variant names:

• chr3-94491352-A-G
• rs4116

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 0.406 in 151,754 control chromosomes in the GnomAD database, including 12,571 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 0.41 (12571 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.898
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.452 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: 0.406 AC: 61539 AN: 151636 Hom.: 12563 Cov.: 32

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.406 AC: 61567 AN: 151754 Hom.: 12571 Cov.: 32 AF XY: 0.404 AC XY: 29931 AN XY: 74154

African (AFR) AF: 0.363 AC: 15016 AN: 41406

American (AMR) AF: 0.429 AC: 6541 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1289 AN: 3468

East Asian (EAS) AF: 0.468 AC: 2413 AN: 5156

South Asian (SAS) AF: 0.440 AC: 2124 AN: 4822

European-Finnish (FIN) AF: 0.398 AC: 4150 AN: 10430

Middle Eastern (MID) AF: 0.288 AC: 84 AN: 292

European-Non Finnish (NFE) AF: 0.424 AC: 28796 AN: 67902

Other (OTH) AF: 0.399 AC: 842 AN: 2110

Alfa AF: 0.273 Hom.: 685

Bravo AF: 0.410

Asia WGS AF: 0.420 AC: 1438 AN: 3426

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.68
PhyloP100		0.90

Splicing

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

Other links and lift over

dbSNP: rs4116; hg19: chr3-94210196;