rs4858060

Variant names:

• chr3-23151204-T-C
• rs4858060

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 0.286 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0821 AC: 3400 AN: 41398

American (AMR) AF: 0.448 AC: 6808 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 898 AN: 3466

East Asian (EAS) AF: 0.332 AC: 1711 AN: 5154

South Asian (SAS) AF: 0.286 AC: 1374 AN: 4800

European-Finnish (FIN) AF: 0.359 AC: 3759 AN: 10468

Middle Eastern (MID) AF: 0.301 AC: 88 AN: 292

European-Non Finnish (NFE) AF: 0.359 AC: 24341 AN: 67812

Other (OTH) AF: 0.295 AC: 618 AN: 2096

Alfa AF: 0.331 Hom.: 6064

Bravo AF: 0.288

Asia WGS AF: 0.304 AC: 1057 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.83
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs4858060; hg19: chr3-23192695;