2-176483297-C-T

Variant names:

• chr2-176483297-C-T
• rs10201330
• ENST00000814385.1:n.88-12176C>T

Variant summary

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

The ENST00000814385.1(LINC01117):​n.88-12176C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0682 in 152,120 control chromosomes in the GnomAD database, including 473 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 0.068 (473 hom., cov: 32)
• Consequence: LINC01117 ENST00000814385.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0836 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000814385.1. 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	ENST00000814385.1		n.88-12176C>T		intron	N/A
	LINC01117	ENST00000814386.1		n.148-12176C>T		intron	N/A
	LINC01117	ENST00000814387.1		n.80-12176C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0682 AC: 10374 AN: 152002 Hom.: 473 Cov.: 32

Gnomad AFR AF: 0.0377

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0593

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.0250

Gnomad SAS AF: 0.0804

Gnomad FIN AF: 0.0732

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0854

Gnomad OTH AF: 0.0869

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

GnomAD4 genome AF: 0.0682 AC: 10377 AN: 152120 Hom.: 473 Cov.: 32 AF XY: 0.0693 AC XY: 5152 AN XY: 74362

African (AFR) AF: 0.0377 AC: 1562 AN: 41486

American (AMR) AF: 0.0593 AC: 906 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 583 AN: 3470

East Asian (EAS) AF: 0.0251 AC: 130 AN: 5178

South Asian (SAS) AF: 0.0800 AC: 385 AN: 4810

European-Finnish (FIN) AF: 0.0732 AC: 774 AN: 10578

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0855 AC: 5811 AN: 68000

Other (OTH) AF: 0.0864 AC: 182 AN: 2106

Alfa AF: 0.0796 Hom.: 1819

Bravo AF: 0.0641

Asia WGS AF: 0.0550 AC: 190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.38
DANN	Benign	0.41
PhyloP100		-0.24

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: rs10201330;

hg19: chr2-177348025;