rs4858060

Positions:

• chr3-23151204-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;