rs4867796

Variant names:

• chr5-175438518-A-C
• rs4867796

Your query was ambiguous. Multiple possible variants found:

• chr5-175438518-A-C
• chr5-175438518-A-T

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 0.171 in 151,972 control chromosomes in the GnomAD database, including 2,286 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 0.17 (2286 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.546

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.197 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: 0.171 AC: 25910 AN: 151854 Hom.: 2286 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.171 AC: 25916 AN: 151972 Hom.: 2286 Cov.: 32 AF XY: 0.173 AC XY: 12817 AN XY: 74264

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.169

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.181

Alfa AF: 0.0418 Hom.: 38

Bravo AF: 0.177

Asia WGS AF: 0.142 AC: 495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.81
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4867796; hg19: chr5-174865521;