rs1447276

Variant names:

• chr5-15364375-G-A
• rs1447276
• ENST00000788346.1:n.265+61200C>T

Variant summary

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

The ENST00000788346.1(LINC02149):​n.265+61200C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 152,148 control chromosomes in the GnomAD database, including 3,549 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 0.20 (3549 hom., cov: 32)
• Consequence: LINC02149 ENST00000788346.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140
• Publications: 10 publications found

Genes affected

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

ENSG00000302688 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.403 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.265+61200C>T		intron_variant	Intron 3 of 5
LINC02149	ENST00000788347.1	n.311+61200C>T		intron_variant	Intron 1 of 1
ENSG00000302688	ENST00000788882.1	n.119+194G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.204 AC: 31069 AN: 152030 Hom.: 3543 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.204 AC: 31087 AN: 152148 Hom.: 3549 Cov.: 32 AF XY: 0.203 AC XY: 15067 AN XY: 74366

African (AFR) AF: 0.142 AC: 5900 AN: 41512

American (AMR) AF: 0.168 AC: 2563 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1025 AN: 3466

East Asian (EAS) AF: 0.418 AC: 2162 AN: 5170

South Asian (SAS) AF: 0.297 AC: 1433 AN: 4822

European-Finnish (FIN) AF: 0.184 AC: 1953 AN: 10592

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15316 AN: 67990

Other (OTH) AF: 0.232 AC: 491 AN: 2112

Alfa AF: 0.222 Hom.: 17450

Bravo AF: 0.198

Asia WGS AF: 0.381 AC: 1325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.21
PhyloP100		0.014

Splicing

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

Other links and lift over

dbSNP: rs1447276; hg19: chr5-15364484;