rs10508158

Variant names:

• chr13-105594775-C-T
• rs10508158
• ENST00000831788.1:n.697-21428G>A

Variant summary

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

The ENST00000831788.1(ENSG00000308108):​n.697-21428G>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: ENSG00000308108 ENST00000831788.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333
• Publications: 1 publications found

Genes affected

ENSG00000308108 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000308108	ENST00000831788.1	n.697-21428G>A		intron_variant	Intron 6 of 6

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

African (AFR) AF: 0.122 AC: 5076 AN: 41470

American (AMR) AF: 0.216 AC: 3296 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 945 AN: 3466

East Asian (EAS) AF: 0.148 AC: 759 AN: 5140

South Asian (SAS) AF: 0.294 AC: 1412 AN: 4806

European-Finnish (FIN) AF: 0.328 AC: 3466 AN: 10562

Middle Eastern (MID) AF: 0.295 AC: 86 AN: 292

European-Non Finnish (NFE) AF: 0.364 AC: 24716 AN: 67948

Other (OTH) AF: 0.278 AC: 587 AN: 2110

Alfa AF: 0.329 Hom.: 14770

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
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs10508158; hg19: chr13-106247124;