rs13017092

Variant names:

• chr2-232420104-C-T
• rs13017092
• ENST00000836072.1:n.31G>A

Variant summary

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

The ENST00000836072.1(ENSG00000237087):​n.31G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 152,158 control chromosomes in the GnomAD database, including 4,258 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 0.21 (4258 hom., cov: 33)
• Consequence: ENSG00000237087 ENST00000836072.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.722
• Publications: 3 publications found

Genes affected

ENSG00000237087 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.29 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
ENSG00000237087	ENST00000836072.1	n.31G>A		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000237087	ENST00000836064.1	n.112-185G>A		intron_variant	Intron 1 of 5
ENSG00000237087	ENST00000836065.1	n.49-185G>A		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32234 AN: 152040 Hom.: 4256 Cov.: 33

Gnomad AFR AF: 0.0671

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.0970

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.212 AC: 32226 AN: 152158 Hom.: 4258 Cov.: 33 AF XY: 0.210 AC XY: 15633 AN XY: 74376

African (AFR) AF: 0.0669 AC: 2782 AN: 41558

American (AMR) AF: 0.202 AC: 3093 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1238 AN: 3470

East Asian (EAS) AF: 0.0967 AC: 498 AN: 5152

South Asian (SAS) AF: 0.194 AC: 934 AN: 4822

European-Finnish (FIN) AF: 0.262 AC: 2770 AN: 10580

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19941 AN: 67962

Other (OTH) AF: 0.231 AC: 488 AN: 2116

Alfa AF: 0.240 Hom.: 580

Bravo AF: 0.203

Asia WGS AF: 0.141 AC: 494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.7
DANN	Benign	0.83
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs13017092; hg19: chr2-233284814;