chr3-107466226-A-G

Variant names:

• chr3-107466226-A-G
• rs1850344

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 0.299 in 152,112 control chromosomes in the GnomAD database, including 7,566 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 0.30 (7566 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.843
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.376 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: 0.299 AC: 45511 AN: 151994 Hom.: 7568 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.299 AC: 45521 AN: 152112 Hom.: 7566 Cov.: 32 AF XY: 0.297 AC XY: 22056 AN XY: 74360

African (AFR) AF: 0.156 AC: 6471 AN: 41512

American (AMR) AF: 0.281 AC: 4299 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1521 AN: 3468

East Asian (EAS) AF: 0.165 AC: 855 AN: 5178

South Asian (SAS) AF: 0.359 AC: 1731 AN: 4824

European-Finnish (FIN) AF: 0.343 AC: 3617 AN: 10560

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.380 AC: 25830 AN: 67978

Other (OTH) AF: 0.322 AC: 679 AN: 2106

Alfa AF: 0.363 Hom.: 16497

Bravo AF: 0.288

Asia WGS AF: 0.259 AC: 904 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.1
DANN	Benign	0.62
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs1850344; hg19: chr3-107185073;