rs1502174

Variant names:

• chr3-135550249-A-G
• rs1502174

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.463 in 152,000 control chromosomes in the GnomAD database, including 16,346 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 0.46 (16346 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.73

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.458 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: 0.463 AC: 70275 AN: 151882 Hom.: 16339 Cov.: 32

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.463 AC: 70308 AN: 152000 Hom.: 16346 Cov.: 32 AF XY: 0.461 AC XY: 34227 AN XY: 74294

Gnomad4 AFR AF: 0.457

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.362

Gnomad4 SAS AF: 0.453

Gnomad4 FIN AF: 0.537

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.468

Alfa AF: 0.464 Hom.: 15163

Bravo AF: 0.458

Asia WGS AF: 0.422 AC: 1467 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	20
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1502174; hg19: chr3-135269091;