3-175812722-C-A

Variant names:

• chr3-175812722-C-A
• rs4894734

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 0.126 in 152,088 control chromosomes in the GnomAD database, including 1,547 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 0.13 (1547 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.690

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.199 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: 0.126 AC: 19076 AN: 151970 Hom.: 1526 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.0927

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0628

Gnomad OTH AF: 0.0993

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

GnomAD4 genome AF: 0.126 AC: 19144 AN: 152088 Hom.: 1547 Cov.: 32 AF XY: 0.130 AC XY: 9644 AN XY: 74354

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.0927

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.0627

Gnomad4 OTH AF: 0.106

Alfa AF: 0.0668 Hom.: 219

Bravo AF: 0.137

Asia WGS AF: 0.179 AC: 624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.21
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4894734; hg19: chr3-175530510;