2-176657649-C-T

Variant names:

• chr2-176657649-C-T
• rs4893911
• ENST00000652227.1:n.494+1871C>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+1871C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 152,114 control chromosomes in the GnomAD database, including 19,592 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 0.47 (19592 hom., cov: 32)
• Consequence: LINC01117 ENST00000652227.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.689
• Publications: 4 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.826 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652227.1. 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
	LINC01117	ENST00000652227.1		n.494+1871C>T		intron	N/A
	LINC01117	ENST00000702503.1		n.369+18076C>T		intron	N/A
	LINC01117	ENST00000702732.2		n.385+18076C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72188 AN: 151996 Hom.: 19581 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.848

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.475 AC: 72208 AN: 152114 Hom.: 19592 Cov.: 32 AF XY: 0.477 AC XY: 35439 AN XY: 74366

African (AFR) AF: 0.206 AC: 8569 AN: 41498

American (AMR) AF: 0.631 AC: 9639 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.530 AC: 1840 AN: 3472

East Asian (EAS) AF: 0.847 AC: 4385 AN: 5176

South Asian (SAS) AF: 0.354 AC: 1707 AN: 4822

European-Finnish (FIN) AF: 0.592 AC: 6256 AN: 10574

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.563 AC: 38289 AN: 67984

Other (OTH) AF: 0.485 AC: 1025 AN: 2112

Alfa AF: 0.540 Hom.: 89830

Bravo AF: 0.474

Asia WGS AF: 0.603 AC: 2097 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	11
DANN	Benign	0.79
PhyloP100		0.69

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4893911;

hg19: chr2-177522377;