rs10508474

Variant names:

• chr10-14489531-T-C
• rs10508474
• ENST00000718707.1:n.106-20981A>G

Variant summary

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

The ENST00000718707.1(ENSG00000293746):​n.106-20981A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.848 in 152,232 control chromosomes in the GnomAD database, including 54,999 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 0.85 (54999 hom., cov: 34)
• Consequence: ENSG00000293746 ENST00000718707.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497
• Publications: 3 publications found

Genes affected

ENSG00000293746 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.859 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
ENSG00000293746	ENST00000718707.1	n.106-20981A>G		intron_variant	Intron 1 of 1
ENSG00000293746	ENST00000718708.1	n.146+19350A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.848 AC: 129014 AN: 152114 Hom.: 54967 Cov.: 34

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.920

Gnomad AMR AF: 0.847

Gnomad ASJ AF: 0.925

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.740

Gnomad FIN AF: 0.855

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.865

Gnomad OTH AF: 0.860

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

GnomAD4 genome AF: 0.848 AC: 129104 AN: 152232 Hom.: 54999 Cov.: 34 AF XY: 0.846 AC XY: 62941 AN XY: 74424

African (AFR) AF: 0.857 AC: 35594 AN: 41544

American (AMR) AF: 0.846 AC: 12950 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.925 AC: 3212 AN: 3472

East Asian (EAS) AF: 0.581 AC: 3004 AN: 5170

South Asian (SAS) AF: 0.741 AC: 3572 AN: 4822

European-Finnish (FIN) AF: 0.855 AC: 9064 AN: 10596

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.865 AC: 58796 AN: 68008

Other (OTH) AF: 0.859 AC: 1816 AN: 2114

Alfa AF: 0.862 Hom.: 92381

Bravo AF: 0.849

Asia WGS AF: 0.694 AC: 2414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.30
DANN	Benign	0.37
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs10508474; hg19: chr10-14531530;