rs10491295

Positions:

• chr5-134872338-G-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 0.0556 in 151,872 control chromosomes in the GnomAD database, including 468 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 0.056 (468 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0555 AC: 8424 AN: 151760 Hom.: 462 Cov.: 32

Gnomad AFR AF: 0.0129

Gnomad AMI AF: 0.0330

Gnomad AMR AF: 0.0751

Gnomad ASJ AF: 0.0395

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.0738

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0493

Gnomad OTH AF: 0.0435

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

GnomAD4 genome AF: 0.0556 AC: 8440 AN: 151872 Hom.: 468 Cov.: 32 AF XY: 0.0619 AC XY: 4593 AN XY: 74242

Gnomad4 AFR AF: 0.0129

Gnomad4 AMR AF: 0.0753

Gnomad4 ASJ AF: 0.0395

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.0738

Gnomad4 NFE AF: 0.0493

Gnomad4 OTH AF: 0.0502

Alfa AF: 0.0532 Hom.: 141

Bravo AF: 0.0521

Asia WGS AF: 0.213 AC: 742 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.8
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491295; hg19: chr5-134208028;