rs4858060

Variant names:

• chr3-23151204-T-C
• rs4858060

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 0.286 in 151,596 control chromosomes in the GnomAD database, including 7,601 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 0.29 (7601 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.427

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.439 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: 0.286 AC: 43344 AN: 151478 Hom.: 7592 Cov.: 29

Gnomad AFR AF: 0.0823

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.286 AC: 43372 AN: 151596 Hom.: 7601 Cov.: 29 AF XY: 0.290 AC XY: 21462 AN XY: 74020

Gnomad4 AFR AF: 0.0821

Gnomad4 AMR AF: 0.448

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.286

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.295

Alfa AF: 0.337 Hom.: 4254

Bravo AF: 0.288

Asia WGS AF: 0.304 AC: 1057 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4858060; hg19: chr3-23192695;