rs1850344

Positions:

• chr3-107466226-A-G

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 0.299 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.380

Gnomad4 OTH AF: 0.322

Alfa AF: 0.372 Hom.: 11749

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1850344; hg19: chr3-107185073;