chr3-135550249-A-G

Variant names:

• chr3-135550249-A-G
• rs1502174

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.457 AC: 18948 AN: 41422

American (AMR) AF: 0.460 AC: 7028 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1662 AN: 3472

East Asian (EAS) AF: 0.362 AC: 1872 AN: 5176

South Asian (SAS) AF: 0.453 AC: 2182 AN: 4812

European-Finnish (FIN) AF: 0.537 AC: 5666 AN: 10552

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.462 AC: 31428 AN: 67976

Other (OTH) AF: 0.468 AC: 990 AN: 2116

Alfa AF: 0.463 Hom.: 22757

Bravo AF: 0.458

Asia WGS AF: 0.422 AC: 1467 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	20
DANN	Benign	0.77
PhyloP100		2.7

Splicing

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

Other links and lift over

dbSNP: rs1502174; hg19: chr3-135269091;