rs10505382

Variant names:

• chr8-120916129-T-G
• rs10505382
• ENST00000517739.1:n.95+2970T>G

Variant summary

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

The ENST00000517739.1(ENSG00000253619):​n.95+2970T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,210 control chromosomes in the GnomAD database, including 1,425 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 0.14 (1425 hom., cov: 32)
• Consequence: ENSG00000253619 ENST00000517739.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.510

Genes affected

ENSG00000253619 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.149 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+2970T>G		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20566 AN: 152092 Hom.: 1421 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.0352

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.135 AC: 20578 AN: 152210 Hom.: 1425 Cov.: 32 AF XY: 0.135 AC XY: 10077 AN XY: 74416

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.0355

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.125

Alfa AF: 0.135 Hom.: 2843

Bravo AF: 0.133

Asia WGS AF: 0.0790 AC: 276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.5
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10505382; hg19: chr8-121928369;