rs10497997

Variant names:

• chr2-213239055-C-T
• rs10497997
• ENST00000730146.1:n.-205G>A

Variant summary

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

The ENST00000730146.1(ENSG00000295442):​n.-205G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0215 in 152,290 control chromosomes in the GnomAD database, including 43 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 0.021 (43 hom., cov: 32)
• Consequence: ENSG00000295442 ENST00000730146.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180
• Publications: 1 publications found

Genes affected

ENSG00000295442 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0516 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
ENSG00000295442	ENST00000730146.1	n.-205G>A		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0215 AC: 3276 AN: 152172 Hom.: 44 Cov.: 32

Gnomad AFR AF: 0.00581

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0195

Gnomad ASJ AF: 0.0570

Gnomad EAS AF: 0.0233

Gnomad SAS AF: 0.0575

Gnomad FIN AF: 0.0262

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0264

Gnomad OTH AF: 0.0288

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

GnomAD4 genome AF: 0.0215 AC: 3274 AN: 152290 Hom.: 43 Cov.: 32 AF XY: 0.0221 AC XY: 1643 AN XY: 74464

African (AFR) AF: 0.00580 AC: 241 AN: 41570

American (AMR) AF: 0.0197 AC: 301 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0570 AC: 198 AN: 3472

East Asian (EAS) AF: 0.0228 AC: 118 AN: 5186

South Asian (SAS) AF: 0.0571 AC: 276 AN: 4830

European-Finnish (FIN) AF: 0.0262 AC: 278 AN: 10614

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0264 AC: 1794 AN: 68010

Other (OTH) AF: 0.0285 AC: 60 AN: 2108

Alfa AF: 0.0214 Hom.: 9

Bravo AF: 0.0200

Asia WGS AF: 0.0420 AC: 147 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	17
DANN	Benign	0.74
PhyloP100		-0.018

Splicing

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

Other links and lift over

dbSNP: rs10497997; hg19: chr2-214103779;