5-179003374-T-C

Variant names:

• chr5-179003374-T-C
• rs2173096

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 0.365 in 152,030 control chromosomes in the GnomAD database, including 10,357 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 0.37 (10357 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370
• Publications: 5 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 (NFE) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55488 AN: 151910 Hom.: 10345 Cov.: 32

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.365 AC: 55527 AN: 152030 Hom.: 10357 Cov.: 32 AF XY: 0.361 AC XY: 26848 AN XY: 74300

African (AFR) AF: 0.373 AC: 15452 AN: 41430

American (AMR) AF: 0.360 AC: 5496 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1179 AN: 3468

East Asian (EAS) AF: 0.191 AC: 989 AN: 5176

South Asian (SAS) AF: 0.192 AC: 925 AN: 4822

European-Finnish (FIN) AF: 0.387 AC: 4083 AN: 10556

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.388 AC: 26396 AN: 67978

Other (OTH) AF: 0.326 AC: 687 AN: 2110

Alfa AF: 0.374 Hom.: 25956

Bravo AF: 0.366

Asia WGS AF: 0.190 AC: 663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.52
PhyloP100		-0.037

Splicing

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

Other links and lift over

dbSNP: rs2173096; hg19: chr5-178430375; COSMIC: COSV73143806;