chr2-188018014-C-T

Variant names:

• chr2-188018014-C-T
• rs10497689
• ENST00000434418.2:n.496+17582G>A

Variant summary

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

The ENST00000772734.1(ENSG00000300562):​n.117-5159C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0697 in 152,168 control chromosomes in the GnomAD database, including 500 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 0.070 (500 hom., cov: 32)
• Consequence: ENSG00000300562 ENST00000772734.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.657
• Publications: 1 publications found

Genes affected

LINC01090 (HGNC:49201): (long intergenic non-protein coding RNA 1090)

ENSG00000300562 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000772734.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01090	ENST00000434418.2	TSL:5	n.496+17582G>A		intron	N/A
	ENSG00000300562	ENST00000772734.1		n.117-5159C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0696 AC: 10578 AN: 152050 Hom.: 497 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.0385

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.0533

Gnomad EAS AF: 0.0377

Gnomad SAS AF: 0.0338

Gnomad FIN AF: 0.0184

Gnomad MID AF: 0.0478

Gnomad NFE AF: 0.0411

Gnomad OTH AF: 0.0761

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

GnomAD4 genome AF: 0.0697 AC: 10607 AN: 152168 Hom.: 500 Cov.: 32 AF XY: 0.0694 AC XY: 5164 AN XY: 74370

African (AFR) AF: 0.125 AC: 5198 AN: 41508

American (AMR) AF: 0.109 AC: 1672 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0533 AC: 185 AN: 3468

East Asian (EAS) AF: 0.0372 AC: 192 AN: 5164

South Asian (SAS) AF: 0.0336 AC: 162 AN: 4824

European-Finnish (FIN) AF: 0.0184 AC: 195 AN: 10604

Middle Eastern (MID) AF: 0.0445 AC: 13 AN: 292

European-Non Finnish (NFE) AF: 0.0410 AC: 2791 AN: 68000

Other (OTH) AF: 0.0777 AC: 164 AN: 2110

Alfa AF: 0.0480 Hom.: 638

Bravo AF: 0.0809

Asia WGS AF: 0.0810 AC: 279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
DANN	Benign	0.38
PhyloP100		0.66
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10497689; hg19: chr2-188882741;