rs10761866

Variant names:

• chr10-64815798-T-C
• rs10761866
• ENST00000718642.1:n.195+796T>C

Variant summary

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

The ENST00000718642.1(ENSG00000293732):​n.195+796T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 151,994 control chromosomes in the GnomAD database, including 3,039 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 0.19 (3039 hom., cov: 32)
• Consequence: ENSG00000293732 ENST00000718642.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.587
• Publications: 5 publications found

Genes affected

ENSG00000293732 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378336	XR_946020.2	n.49+796T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293732	ENST00000718642.1	n.195+796T>C		intron_variant	Intron 2 of 6
ENSG00000293732	ENST00000718643.1	n.362+796T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29580 AN: 151876 Hom.: 3039 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.271

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.195 AC: 29589 AN: 151994 Hom.: 3039 Cov.: 32 AF XY: 0.200 AC XY: 14836 AN XY: 74270

African (AFR) AF: 0.124 AC: 5147 AN: 41512

American (AMR) AF: 0.147 AC: 2243 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 688 AN: 3472

East Asian (EAS) AF: 0.253 AC: 1307 AN: 5160

South Asian (SAS) AF: 0.270 AC: 1298 AN: 4816

European-Finnish (FIN) AF: 0.285 AC: 3014 AN: 10566

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.225 AC: 15257 AN: 67922

Other (OTH) AF: 0.196 AC: 412 AN: 2106

Alfa AF: 0.197 Hom.: 682

Bravo AF: 0.179

Asia WGS AF: 0.223 AC: 771 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	10
DANN	Benign	0.82
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs10761866; hg19: chr10-66575555;