rs10508626

Variant names:

• chr10-20428860-C-T
• rs10508626
• ENST00000785943.1:n.285+58105C>T

Variant summary

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

The ENST00000785943.1(ENSG00000302338):​n.285+58105C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,022 control chromosomes in the GnomAD database, including 1,099 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 0.11 (1099 hom., cov: 33)
• Consequence: ENSG00000302338 ENST00000785943.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780
• Publications: 1 publications found

Genes affected

ENSG00000302338 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.163 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
ENSG00000302338	ENST00000785943.1	n.285+58105C>T		intron_variant	Intron 1 of 5
ENSG00000302338	ENST00000785944.1	n.198+58105C>T		intron_variant	Intron 1 of 3
ENSG00000302338	ENST00000785945.1	n.132+58105C>T		intron_variant	Intron 1 of 4
ENSG00000302338	ENST00000785947.1	n.41+58105C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17372 AN: 151904 Hom.: 1097 Cov.: 33

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.0736

Gnomad AMR AF: 0.0909

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0593

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0968

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.114 AC: 17385 AN: 152022 Hom.: 1099 Cov.: 33 AF XY: 0.112 AC XY: 8301 AN XY: 74322

African (AFR) AF: 0.167 AC: 6909 AN: 41440

American (AMR) AF: 0.0908 AC: 1386 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 404 AN: 3470

East Asian (EAS) AF: 0.118 AC: 610 AN: 5162

South Asian (SAS) AF: 0.111 AC: 533 AN: 4816

European-Finnish (FIN) AF: 0.0593 AC: 626 AN: 10564

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0968 AC: 6582 AN: 67978

Other (OTH) AF: 0.109 AC: 230 AN: 2116

Alfa AF: 0.104 Hom.: 1225

Bravo AF: 0.121

Asia WGS AF: 0.139 AC: 484 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.7
DANN	Benign	0.57
PhyloP100		0.078

Splicing

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

Other links and lift over

dbSNP: rs10508626; hg19: chr10-20717789;