rs2969344

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

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	ENST00000652995.1	n.398+20066G>A		intron_variant	Intron 2 of 3

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

Gnomad4 AFR AF: 0.0586

Gnomad4 AMR AF: 0.0937

Gnomad4 ASJ AF: 0.0919

Gnomad4 EAS AF: 0.0267

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.100

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.109

Alfa AF: 0.111 Hom.: 578

Bravo AF: 0.0916

Asia WGS AF: 0.107 AC: 372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2969344; hg19: chr2-177382589;