10-93751506-C-T

Variant names:

• chr10-93751506-C-T
• rs2095890
• XR_246160.5:n.238-1522G>A

Variant summary

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

The XR_246160.5(LOC101927013):​n.238-1522G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 151,950 control chromosomes in the GnomAD database, including 5,612 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 0.24 (5612 hom., cov: 31)
• Consequence: LOC101927013 XR_246160.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.568

Genes affected

LOC101927013 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927013	XR_246160.5	n.238-1522G>A		intron_variant	Intron 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36914 AN: 151832 Hom.: 5599 Cov.: 31

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.0969

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.243 AC: 36958 AN: 151950 Hom.: 5612 Cov.: 31 AF XY: 0.233 AC XY: 17329 AN XY: 74264

Gnomad4 AFR AF: 0.421

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.0969

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.255

Alfa AF: 0.0783 Hom.: 95

Bravo AF: 0.258

Asia WGS AF: 0.120 AC: 421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.3
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2095890; hg19: chr10-95511263;