rs251934

Variant names:

• chr5-175351675-A-G
• rs251934

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 0.339 in 152,064 control chromosomes in the GnomAD database, including 9,321 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 0.34 (9321 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.450

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.403 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: 0.339 AC: 51446 AN: 151946 Hom.: 9314 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.339 AC: 51474 AN: 152064 Hom.: 9321 Cov.: 32 AF XY: 0.335 AC XY: 24916 AN XY: 74318

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.413

Gnomad4 NFE AF: 0.407

Gnomad4 OTH AF: 0.370

Alfa AF: 0.384 Hom.: 5981

Bravo AF: 0.326

Asia WGS AF: 0.210 AC: 736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs251934; hg19: chr5-174778678; COSMIC: COSV50192838;