ENST00000652227.1:n.494+28991C>T

Variant names:

• chr2-176684769-C-T
• rs868179
• ENST00000652227.1:n.494+28991C>T

Variant summary

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

The ENST00000652227.1(LINC01117):​n.494+28991C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 152,142 control chromosomes in the GnomAD database, including 9,564 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 0.25 (9564 hom., cov: 32)
• Consequence: LINC01117 ENST00000652227.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.110
• Publications: 13 publications found

Genes affected

LINC01117 (HGNC:49260): (long intergenic non-protein coding RNA 1117)

ENSG00000230552 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.64 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
LINC01117	ENST00000652227.1	n.494+28991C>T		intron_variant	Intron 4 of 5
LINC01117	ENST00000702503.1	n.369+45196C>T		intron_variant	Intron 2 of 4
LINC01117	ENST00000702732.2	n.385+45196C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38619 AN: 152026 Hom.: 9524 Cov.: 32

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.0110

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.0600

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.0925

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.254 AC: 38720 AN: 152142 Hom.: 9564 Cov.: 32 AF XY: 0.252 AC XY: 18779 AN XY: 74392

African (AFR) AF: 0.646 AC: 26783 AN: 41450

American (AMR) AF: 0.148 AC: 2263 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 445 AN: 3472

East Asian (EAS) AF: 0.0110 AC: 57 AN: 5182

South Asian (SAS) AF: 0.286 AC: 1380 AN: 4824

European-Finnish (FIN) AF: 0.0600 AC: 636 AN: 10592

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.0925 AC: 6291 AN: 68014

Other (OTH) AF: 0.231 AC: 489 AN: 2114

Alfa AF: 0.120 Hom.: 4942

Bravo AF: 0.275

Asia WGS AF: 0.194 AC: 679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.9
DANN	Benign	0.59
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs868179; hg19: chr2-177549497;