rs4858957

Variant names:

• chr3-87360008-A-G
• rs4858957

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 0.305 in 152,020 control chromosomes in the GnomAD database, including 8,770 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 0.30 (8770 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.665
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.423 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: 0.305 AC: 46287 AN: 151902 Hom.: 8771 Cov.: 31

Gnomad AFR AF: 0.0775

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.305 AC: 46291 AN: 152020 Hom.: 8770 Cov.: 31 AF XY: 0.300 AC XY: 22317 AN XY: 74290

African (AFR) AF: 0.0773 AC: 3207 AN: 41502

American (AMR) AF: 0.328 AC: 5003 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1294 AN: 3468

East Asian (EAS) AF: 0.219 AC: 1130 AN: 5158

South Asian (SAS) AF: 0.289 AC: 1392 AN: 4824

European-Finnish (FIN) AF: 0.374 AC: 3952 AN: 10562

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.428 AC: 29053 AN: 67942

Other (OTH) AF: 0.320 AC: 674 AN: 2108

Alfa AF: 0.360 Hom.: 6974

Bravo AF: 0.292

Asia WGS AF: 0.255 AC: 889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.9
DANN	Benign	0.68
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs4858957; hg19: chr3-87409158;