rs10494232

Variant names:

• chr1-119816127-C-T
• rs10494232
• ENST00000743334.1:n.-110C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000743334.1(ENSG00000296885):​n.-110C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0198 in 152,186 control chromosomes in the GnomAD database, including 42 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 0.020 (42 hom., cov: 32)
• Consequence: ENSG00000296885 ENST00000743334.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.31
• Publications: 0 publications found

Genes affected

ENSG00000296885 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0198 (3009/152186) while in subpopulation AFR AF = 0.0362 (1501/41510). AF 95% confidence interval is 0.0346. There are 42 homozygotes in GnomAd4. There are 1426 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 42 gene

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
ENSG00000296885	ENST00000743334.1	n.-110C>T		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0198 AC: 3005 AN: 152068 Hom.: 42 Cov.: 32

Gnomad AFR AF: 0.0362

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.0147

Gnomad ASJ AF: 0.0401

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0104

Gnomad FIN AF: 0.00170

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0132

Gnomad OTH AF: 0.0158

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

GnomAD4 genome AF: 0.0198 AC: 3009 AN: 152186 Hom.: 42 Cov.: 32 AF XY: 0.0192 AC XY: 1426 AN XY: 74388

African (AFR) AF: 0.0362 AC: 1501 AN: 41510

American (AMR) AF: 0.0147 AC: 224 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0401 AC: 139 AN: 3470

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5166

South Asian (SAS) AF: 0.0108 AC: 52 AN: 4818

European-Finnish (FIN) AF: 0.00170 AC: 18 AN: 10594

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0132 AC: 899 AN: 68022

Other (OTH) AF: 0.0156 AC: 33 AN: 2112

Alfa AF: 0.0199 Hom.: 21

Bravo AF: 0.0217

Asia WGS AF: 0.00549 AC: 19 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.8
DANN	Benign	0.66
PhyloP100		2.3

Splicing

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

Other links and lift over

dbSNP: rs10494232; hg19: chr1-120358750;