rs977762

Positions:

• chr5-15169346-C-T

Variant summary

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

The ENST00000651224.1(LINC02149):​n.311+22923G>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 0.329 in 151,986 control chromosomes in the GnomAD database, including 8,653 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 0.33 (8653 hom., cov: 32)
• Consequence: LINC02149 ENST00000651224.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0850

Genes affected

LINC02149 (HGNC:53010): (long intergenic non-protein coding RNA 2149)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02149	ENST00000651224.1	n.311+22923G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.329 AC: 50040 AN: 151868 Hom.: 8661 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.329 AC: 50042 AN: 151986 Hom.: 8653 Cov.: 32 AF XY: 0.324 AC XY: 24058 AN XY: 74284

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.300

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.353

Alfa AF: 0.363 Hom.: 1269

Bravo AF: 0.318

Asia WGS AF: 0.191 AC: 667 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.0
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs977762; hg19: chr5-15169455; COSMIC: COSV68636758;