10-117820091-T-C

Variant names:

• chr10-117820091-T-C
• rs10886146
• ENST00000820289.1:n.237+6970A>G

Variant summary

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

The ENST00000820289.1(ENSG00000263041):​n.237+6970A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 152,024 control chromosomes in the GnomAD database, including 17,577 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 0.44 (17577 hom., cov: 32)
• Consequence: ENSG00000263041 ENST00000820289.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.49
• Publications: 3 publications found

Genes affected

ENSG00000263041 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.572 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
ENSG00000263041	ENST00000820289.1	n.237+6970A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67355 AN: 151906 Hom.: 17581 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.443 AC: 67349 AN: 152024 Hom.: 17577 Cov.: 32 AF XY: 0.442 AC XY: 32825 AN XY: 74286

African (AFR) AF: 0.145 AC: 6034 AN: 41518

American (AMR) AF: 0.492 AC: 7512 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.582 AC: 2021 AN: 3470

East Asian (EAS) AF: 0.501 AC: 2587 AN: 5168

South Asian (SAS) AF: 0.590 AC: 2837 AN: 4812

European-Finnish (FIN) AF: 0.502 AC: 5278 AN: 10516

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.576 AC: 39168 AN: 67958

Other (OTH) AF: 0.469 AC: 986 AN: 2102

Alfa AF: 0.503 Hom.: 8521

Bravo AF: 0.426

Asia WGS AF: 0.493 AC: 1718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	18
DANN	Benign	0.71
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs10886146; hg19: chr10-119579602;