5-179003374-T-C

Variant names:

• chr5-179003374-T-C
• rs2173096

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 0.365 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.365 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

Gnomad4 AFR AF: 0.373

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.340

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.387

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.326

Alfa AF: 0.376 Hom.: 17057

Bravo AF: 0.366

Asia WGS AF: 0.190 AC: 663 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	2.4
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

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