rs10508158

Variant names:

• chr13-105594775-C-T
• rs10508158
• XR_931698.2:n.731-21428G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_931698.2(LOC105370345):​n.731-21428G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 151,950 control chromosomes in the GnomAD database, including 6,274 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 0.27 (6274 hom., cov: 32)
• Consequence: LOC105370345 XR_931698.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333

Genes affected

LOC105370345 (HGNC:):

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 = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370345	XR_931698.2	n.731-21428G>A		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40550 AN: 151832 Hom.: 6267 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.267 AC: 40576 AN: 151950 Hom.: 6274 Cov.: 32 AF XY: 0.263 AC XY: 19564 AN XY: 74254

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.328

Gnomad4 NFE AF: 0.364

Gnomad4 OTH AF: 0.278

Alfa AF: 0.338 Hom.: 12180

Bravo AF: 0.250

Asia WGS AF: 0.208 AC: 729 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	1.0
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10508158; hg19: chr13-106247124;