rs4974501

Variant names:

• chr3-134391019-C-A
• rs4974501

Your query was ambiguous. Multiple possible variants found:

• chr3-134391019-C-A
• chr3-134391019-C-T

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 0.354 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.232 AC: 9569 AN: 41286

American (AMR) AF: 0.441 AC: 6722 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1469 AN: 3466

East Asian (EAS) AF: 0.391 AC: 1993 AN: 5100

South Asian (SAS) AF: 0.429 AC: 2058 AN: 4800

European-Finnish (FIN) AF: 0.377 AC: 3963 AN: 10504

Middle Eastern (MID) AF: 0.448 AC: 130 AN: 290

European-Non Finnish (NFE) AF: 0.391 AC: 26582 AN: 67926

Other (OTH) AF: 0.353 AC: 740 AN: 2094

Alfa AF: 0.380 Hom.: 16097

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
PhyloP100		-0.027

Splicing

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

Other links and lift over

dbSNP: rs4974501; hg19: chr3-134109861;