rs10161791

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000285534 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000285534	ENST00000650264.1	n.759-58284T>C		intron_variant	Intron 1 of 3

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

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.198

Alfa AF: 0.178 Hom.: 4165

Bravo AF: 0.192

Asia WGS AF: 0.280 AC: 971 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10161791; hg19: chr13-110281789;