rs745978

Variant names:

• chr5-15285305-T-C
• rs745978
• ENST00000788346.1:n.266-41538A>G

Variant summary

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

The ENST00000788346.1(LINC02149):​n.266-41538A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0429 in 152,204 control chromosomes in the GnomAD database, including 284 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 0.043 (284 hom., cov: 32)
• Consequence: LINC02149 ENST00000788346.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.430
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.174 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	ENST00000788346.1	n.266-41538A>G		intron_variant	Intron 3 of 5
LINC02149	ENST00000788347.1	n.312-41538A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0429 AC: 6524 AN: 152086 Hom.: 285 Cov.: 32

Gnomad AFR AF: 0.0872

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0225

Gnomad ASJ AF: 0.00606

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.0284

Gnomad FIN AF: 0.00811

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0184

Gnomad OTH AF: 0.0311

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

GnomAD4 genome AF: 0.0429 AC: 6522 AN: 152204 Hom.: 284 Cov.: 32 AF XY: 0.0423 AC XY: 3150 AN XY: 74422

African (AFR) AF: 0.0870 AC: 3612 AN: 41506

American (AMR) AF: 0.0224 AC: 343 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00606 AC: 21 AN: 3468

East Asian (EAS) AF: 0.184 AC: 955 AN: 5186

South Asian (SAS) AF: 0.0284 AC: 137 AN: 4826

European-Finnish (FIN) AF: 0.00811 AC: 86 AN: 10606

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0184 AC: 1253 AN: 68002

Other (OTH) AF: 0.0303 AC: 64 AN: 2110

Alfa AF: 0.0286 Hom.: 401

Bravo AF: 0.0476

Asia WGS AF: 0.0740 AC: 257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.4
DANN	Benign	0.54
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs745978; hg19: chr5-15285414;