rs10161791

Variant names:

• chr13-109629442-A-G
• rs10161791
• ENST00000650264.1:n.759-58284T>C

Variant summary

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

The ENST00000650264.1(ENSG00000285534):​n.759-58284T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,128 control chromosomes in the GnomAD database, including 3,021 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 0.20 (3021 hom., cov: 32)
• Consequence: ENSG00000285534 ENST00000650264.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 4 publications found

Genes affected

ENSG00000285534 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650264.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285534	ENST00000650264.1		n.759-58284T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29832 AN: 152010 Hom.: 3010 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.196 AC: 29880 AN: 152128 Hom.: 3021 Cov.: 32 AF XY: 0.195 AC XY: 14539 AN XY: 74382

African (AFR) AF: 0.239 AC: 9897 AN: 41492

American (AMR) AF: 0.123 AC: 1886 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 878 AN: 3470

East Asian (EAS) AF: 0.297 AC: 1533 AN: 5158

South Asian (SAS) AF: 0.225 AC: 1088 AN: 4828

European-Finnish (FIN) AF: 0.192 AC: 2030 AN: 10596

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11912 AN: 67972

Other (OTH) AF: 0.198 AC: 419 AN: 2116

Alfa AF: 0.181 Hom.: 9919

Bravo AF: 0.192

Asia WGS AF: 0.280 AC: 971 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.082
DANN	Benign	0.17
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs10161791; hg19: chr13-110281789;