rs10508150

Variant names:

• chr13-104876171-G-A
• rs10508150
• ENST00000841827.1:n.164+8433G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000841827.1(ENSG00000309518):​n.164+8433G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0257 in 152,190 control chromosomes in the GnomAD database, including 132 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 0.026 (132 hom., cov: 32)
• Consequence: ENSG00000309518 ENST00000841827.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.175
• Publications: 1 publications found

Genes affected

ENSG00000309518 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0774 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984608	XR_001749997.2	n.128-14126G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309518	ENST00000841827.1	n.164+8433G>A		intron_variant	Intron 1 of 1
ENSG00000309518	ENST00000841828.1	n.242+7002G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0257 AC: 3909 AN: 152072 Hom.: 131 Cov.: 32

Gnomad AFR AF: 0.00512

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0806

Gnomad ASJ AF: 0.00923

Gnomad EAS AF: 0.0461

Gnomad SAS AF: 0.0108

Gnomad FIN AF: 0.0720

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0195

Gnomad OTH AF: 0.0254

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

GnomAD4 genome AF: 0.0257 AC: 3918 AN: 152190 Hom.: 132 Cov.: 32 AF XY: 0.0290 AC XY: 2156 AN XY: 74390

African (AFR) AF: 0.00510 AC: 212 AN: 41540

American (AMR) AF: 0.0812 AC: 1241 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.00923 AC: 32 AN: 3468

East Asian (EAS) AF: 0.0461 AC: 238 AN: 5168

South Asian (SAS) AF: 0.0108 AC: 52 AN: 4822

European-Finnish (FIN) AF: 0.0720 AC: 762 AN: 10588

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0195 AC: 1328 AN: 68000

Other (OTH) AF: 0.0251 AC: 53 AN: 2112

Alfa AF: 0.0223 Hom.: 17

Bravo AF: 0.0280

Asia WGS AF: 0.0280 AC: 96 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.64
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs10508150; hg19: chr13-105528522;