rs2457174

chr5-133843389-C-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 0.328 in 152,002 control chromosomes in the GnomAD database, including 9,125 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 0.33 (9125 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49779 AN: 151884 Hom.: 9125 Cov.: 31

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.0427

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.328 AC: 49785 AN: 152002 Hom.: 9125 Cov.: 31 AF XY: 0.318 AC XY: 23593 AN XY: 74288

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.0426

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.333

Alfa AF: 0.403 Hom.: 19323

Bravo AF: 0.319

Asia WGS AF: 0.120 AC: 420 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	7.6
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2457174; hg19: chr5-133179080;