10-8352117-A-G

Variant names:

• chr10-8352117-A-G
• rs10905349
• ENST00000798205.1:n.112-12592A>G

Variant summary

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

The ENST00000798205.1(ENSG00000226990):​n.112-12592A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.756 in 151,996 control chromosomes in the GnomAD database, including 44,210 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 0.76 (44210 hom., cov: 31)
• Consequence: ENSG00000226990 ENST00000798205.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.943
• Publications: 4 publications found

Genes affected

ENSG00000226990 (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 (SAS) allele frequency at 95% confidence interval = 0.84 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
ENSG00000226990	ENST00000798205.1	n.112-12592A>G		intron_variant	Intron 1 of 5
ENSG00000226990	ENST00000798206.1	n.52+8531A>G		intron_variant	Intron 1 of 3
ENSG00000303957	ENST00000798382.1	n.204+1852T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.756 AC: 114883 AN: 151878 Hom.: 44163 Cov.: 31

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.872

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.862

Gnomad FIN AF: 0.833

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.801

Gnomad OTH AF: 0.792

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

GnomAD4 genome AF: 0.756 AC: 114983 AN: 151996 Hom.: 44210 Cov.: 31 AF XY: 0.758 AC XY: 56336 AN XY: 74282

African (AFR) AF: 0.661 AC: 27387 AN: 41404

American (AMR) AF: 0.793 AC: 12118 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.872 AC: 3028 AN: 3472

East Asian (EAS) AF: 0.469 AC: 2414 AN: 5142

South Asian (SAS) AF: 0.862 AC: 4156 AN: 4820

European-Finnish (FIN) AF: 0.833 AC: 8797 AN: 10564

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.801 AC: 54436 AN: 67986

Other (OTH) AF: 0.794 AC: 1676 AN: 2112

Alfa AF: 0.787 Hom.: 91480

Bravo AF: 0.749

Asia WGS AF: 0.699 AC: 2433 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	7.4
DANN	Benign	0.45
PhyloP100		0.94

Splicing

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

Other links and lift over

dbSNP: rs10905349; hg19: chr10-8394080;