ENST00000449086.5:n.779+735G>T

Variant names:

• chr2-19874099-G-T
• rs11096626
• ENST00000449086.5:n.779+735G>T

Variant summary

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

The ENST00000449086.5(LINC00954):​n.779+735G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 152,062 control chromosomes in the GnomAD database, including 12,737 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 0.41 (12737 hom., cov: 33)
• Consequence: LINC00954 ENST00000449086.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.319
• Publications: 3 publications found

Genes affected

LINC00954 (HGNC:48668): (long intergenic non-protein coding RNA 954)

ACMG classification

Our verdict: Benign. The variant received -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 = 0.472 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000449086.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00954	NR_033875.1		n.799+735G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00954	ENST00000449086.5	TSL:1	n.779+735G>T		intron	N/A
	LINC00954	ENST00000433669.2	TSL:2	n.756+735G>T		intron	N/A
	LINC00954	ENST00000607100.5	TSL:2	n.648+735G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61601 AN: 151944 Hom.: 12725 Cov.: 33

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.406 AC: 61667 AN: 152062 Hom.: 12737 Cov.: 33 AF XY: 0.407 AC XY: 30223 AN XY: 74344

African (AFR) AF: 0.477 AC: 19789 AN: 41464

American (AMR) AF: 0.373 AC: 5711 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1312 AN: 3466

East Asian (EAS) AF: 0.421 AC: 2179 AN: 5172

South Asian (SAS) AF: 0.417 AC: 2011 AN: 4826

European-Finnish (FIN) AF: 0.332 AC: 3509 AN: 10558

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.379 AC: 25755 AN: 67964

Other (OTH) AF: 0.415 AC: 875 AN: 2110

Alfa AF: 0.391 Hom.: 35785

Bravo AF: 0.407

Asia WGS AF: 0.418 AC: 1454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.55
DANN	Benign	0.44
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs11096626; hg19: chr2-20073860;