rs4701170

Variant names:

• chr5-179470589-G-A
• rs4701170

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 0.191 in 152,220 control chromosomes in the GnomAD database, including 3,743 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 0.19 (3743 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.456 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: 0.191 AC: 29005 AN: 152102 Hom.: 3726 Cov.: 33

Gnomad AFR AF: 0.0856

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.191 AC: 29039 AN: 152220 Hom.: 3743 Cov.: 33 AF XY: 0.199 AC XY: 14846 AN XY: 74418

African (AFR) AF: 0.0855 AC: 3553 AN: 41560

American (AMR) AF: 0.381 AC: 5826 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 540 AN: 3470

East Asian (EAS) AF: 0.471 AC: 2430 AN: 5156

South Asian (SAS) AF: 0.323 AC: 1561 AN: 4826

European-Finnish (FIN) AF: 0.208 AC: 2203 AN: 10610

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12309 AN: 67996

Other (OTH) AF: 0.191 AC: 404 AN: 2116

Alfa AF: 0.182 Hom.: 4869

Bravo AF: 0.201

Asia WGS AF: 0.416 AC: 1444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.13
DANN	Benign	0.71
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4701170; hg19: chr5-178897590; COSMIC: COSV74069005;