rs10501162

Variant names:

• chr11-36725205-C-A
• rs10501162
• XR_001748187.1:n.576+14398C>A

Variant summary

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

The XR_001748187.1(LOC107984326):​n.576+14398C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,144 control chromosomes in the GnomAD database, including 2,438 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 0.17 (2438 hom., cov: 32)
• Consequence: LOC107984326 XR_001748187.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.260

Genes affected

LOC107984326 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984326	XR_001748187.1	n.576+14398C>A		intron_variant	Intron 3 of 3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25891 AN: 152026 Hom.: 2439 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.170 AC: 25904 AN: 152144 Hom.: 2438 Cov.: 32 AF XY: 0.170 AC XY: 12620 AN XY: 74390

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.156

Alfa AF: 0.155 Hom.: 330

Bravo AF: 0.171

Asia WGS AF: 0.163 AC: 566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.9
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10501162; hg19: chr11-36746755;