rs2969344

Variant names:

• chr2-176517861-G-A
• rs2969344
• ENST00000652995.1:n.398+20066G>A

Variant summary

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

The ENST00000652995.1(LINC01117):​n.398+20066G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0957 in 152,186 control chromosomes in the GnomAD database, including 779 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 0.096 (779 hom., cov: 32)
• Consequence: LINC01117 ENST00000652995.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336
• Publications: 4 publications found

Genes affected

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

ENSG00000306098 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652995.1. 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	ENST00000652995.1		n.398+20066G>A		intron	N/A
	LINC01117	ENST00000814385.1		n.185+22291G>A		intron	N/A
	LINC01117	ENST00000814386.1		n.245+22291G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0957 AC: 14553 AN: 152068 Hom.: 777 Cov.: 32

Gnomad AFR AF: 0.0585

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0937

Gnomad ASJ AF: 0.0919

Gnomad EAS AF: 0.0266

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.0957 AC: 14569 AN: 152186 Hom.: 779 Cov.: 32 AF XY: 0.0950 AC XY: 7071 AN XY: 74398

African (AFR) AF: 0.0586 AC: 2435 AN: 41522

American (AMR) AF: 0.0937 AC: 1432 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0919 AC: 319 AN: 3470

East Asian (EAS) AF: 0.0267 AC: 138 AN: 5176

South Asian (SAS) AF: 0.162 AC: 779 AN: 4812

European-Finnish (FIN) AF: 0.100 AC: 1059 AN: 10590

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8112 AN: 68018

Other (OTH) AF: 0.109 AC: 230 AN: 2106

Alfa AF: 0.107 Hom.: 2037

Bravo AF: 0.0916

Asia WGS AF: 0.107 AC: 372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	5.1
DANN	Benign	0.74
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs2969344; hg19: chr2-177382589;