rs977762

Variant names:

• chr5-15169346-C-T
• rs977762
• ENST00000651224.1:n.311+22923G>A

Variant summary

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

The ENST00000651224.1(LINC02149):​n.311+22923G>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0850
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02149	ENST00000651224.1	n.311+22923G>A		intron_variant	Intron 2 of 3
LINC02149	ENST00000788346.1	n.586+22923G>A		intron_variant	Intron 5 of 5
LINC02149	ENST00000788348.1	n.170+22935G>A		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.231 AC: 9590 AN: 41466

American (AMR) AF: 0.300 AC: 4585 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1499 AN: 3470

East Asian (EAS) AF: 0.170 AC: 876 AN: 5162

South Asian (SAS) AF: 0.223 AC: 1076 AN: 4818

European-Finnish (FIN) AF: 0.377 AC: 3979 AN: 10550

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27229 AN: 67936

Other (OTH) AF: 0.353 AC: 747 AN: 2114

Alfa AF: 0.358 Hom.: 1293

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
PhyloP100		-0.085

Splicing

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

Other links and lift over

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