rs10505381

Variant names:

• chr8-120914915-C-T
• rs10505381
• ENST00000517739.1:n.95+1756C>T

Variant summary

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

The ENST00000517739.1(ENSG00000253619):​n.95+1756C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0426 in 152,150 control chromosomes in the GnomAD database, including 253 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 0.043 (253 hom., cov: 32)
• Consequence: ENSG00000253619 ENST00000517739.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.597
• Publications: 1 publications found

Genes affected

ENSG00000253619 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.127 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253619	ENST00000517739.1	n.95+1756C>T		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.0425 AC: 6460 AN: 152032 Hom.: 252 Cov.: 32

Gnomad AFR AF: 0.0833

Gnomad AMI AF: 0.0429

Gnomad AMR AF: 0.0396

Gnomad ASJ AF: 0.0222

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.0251

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0105

Gnomad OTH AF: 0.0397

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

GnomAD4 genome AF: 0.0426 AC: 6481 AN: 152150 Hom.: 253 Cov.: 32 AF XY: 0.0449 AC XY: 3342 AN XY: 74396

African (AFR) AF: 0.0835 AC: 3466 AN: 41492

American (AMR) AF: 0.0395 AC: 603 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0222 AC: 77 AN: 3470

East Asian (EAS) AF: 0.135 AC: 696 AN: 5160

South Asian (SAS) AF: 0.107 AC: 516 AN: 4830

European-Finnish (FIN) AF: 0.0251 AC: 266 AN: 10600

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0105 AC: 712 AN: 68002

Other (OTH) AF: 0.0412 AC: 87 AN: 2112

Alfa AF: 0.0294 Hom.: 21

Bravo AF: 0.0436

Asia WGS AF: 0.135 AC: 468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.1
DANN	Benign	0.78
PhyloP100		0.60
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10505381; hg19: chr8-121927155;