rs13027120

Variant names:

• chr2-218156191-T-C
• rs13027120
• ENST00000811769.1:n.46A>G

Variant summary

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

The ENST00000811769.1(ENSG00000305582):​n.46A>G 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 0.599 in 151,974 control chromosomes in the GnomAD database, including 28,890 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 0.60 (28890 hom., cov: 31)
• Consequence: ENSG00000305582 ENST00000811769.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.581
• Publications: 14 publications found

Genes affected

ENSG00000305582 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000811769.1. 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
	ENSG00000305582	ENST00000811769.1		n.46A>G		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000305582	ENST00000811770.1		n.46A>G		non_coding_transcript_exon	Exon 1 of 4

Frequencies

GnomAD3 genomes AF: 0.599 AC: 91008 AN: 151856 Hom.: 28847 Cov.: 31

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.599 AC: 91089 AN: 151974 Hom.: 28890 Cov.: 31 AF XY: 0.594 AC XY: 44160 AN XY: 74288

African (AFR) AF: 0.805 AC: 33387 AN: 41466

American (AMR) AF: 0.558 AC: 8522 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.655 AC: 2272 AN: 3468

East Asian (EAS) AF: 0.283 AC: 1459 AN: 5152

South Asian (SAS) AF: 0.576 AC: 2774 AN: 4820

European-Finnish (FIN) AF: 0.431 AC: 4549 AN: 10546

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.529 AC: 35960 AN: 67940

Other (OTH) AF: 0.613 AC: 1294 AN: 2110

Alfa AF: 0.576 Hom.: 12188

Bravo AF: 0.614

Asia WGS AF: 0.449 AC: 1564 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	13
DANN	Benign	0.71
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs13027120; hg19: chr2-219020914;