rs868179

Positions:

• chr2-176684769-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000702503.1(LINC01117):​n.369+45196C>T 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 0.254 in 152,142 control chromosomes in the GnomAD database, including 9,564 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 0.25 (9564 hom., cov: 32)
• Consequence: LINC01117 ENST00000702503.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.110

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.64 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	ENST00000702503.1	n.369+45196C>T		intron_variant, non_coding_transcript_variant
LINC01117	ENST00000652227.1	n.494+28991C>T		intron_variant, non_coding_transcript_variant
LINC01117	ENST00000702732.1	n.346+45196C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38619 AN: 152026 Hom.: 9524 Cov.: 32

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.0110

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.0600

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.0925

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.254 AC: 38720 AN: 152142 Hom.: 9564 Cov.: 32 AF XY: 0.252 AC XY: 18779 AN XY: 74392

Gnomad4 AFR AF: 0.646

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.0110

Gnomad4 SAS AF: 0.286

Gnomad4 FIN AF: 0.0600

Gnomad4 NFE AF: 0.0925

Gnomad4 OTH AF: 0.231

Alfa AF: 0.113 Hom.: 3350

Bravo AF: 0.275

Asia WGS AF: 0.194 AC: 679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.9
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs868179; hg19: chr2-177549497;