rs2969344

Positions:

• chr2-176517861-G-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01117	ENST00000652995.1	n.398+20066G>A		intron_variant, non_coding_transcript_variant

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;