rs13175726

Variant names:

• chr5-97051329-A-G
• rs13175726

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 0.305 in 152,030 control chromosomes in the GnomAD database, including 7,366 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 0.31 (7366 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740

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 (AFR) allele frequency at 95% confidence interval = 0.391 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: 0.305 AC: 46367 AN: 151912 Hom.: 7350 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.305 AC: 46434 AN: 152030 Hom.: 7366 Cov.: 32 AF XY: 0.302 AC XY: 22453 AN XY: 74358

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.298

Alfa AF: 0.286 Hom.: 10957

Bravo AF: 0.307

Asia WGS AF: 0.326 AC: 1134 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	3.3
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: rs13175726; hg19: chr5-96387033; COSMIC: COSV60168164;