rs4974501

chr3-134391019-C-Achr3-134391019-C-T

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 0.354 in 151,602 control chromosomes in the GnomAD database, including 9,999 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 0.35 (9999 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53639 AN: 151484 Hom.: 9990 Cov.: 30

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.429

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.354 AC: 53657 AN: 151602 Hom.: 9999 Cov.: 30 AF XY: 0.357 AC XY: 26412 AN XY: 74040

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.424

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.353

Alfa AF: 0.382 Hom.: 12386

Bravo AF: 0.354

Asia WGS AF: 0.399 AC: 1383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.69
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: rs4974501; hg19: chr3-134109861;