13-54041594-C-T

Variant names:

• chr13-54041594-C-T
• rs9596897
• ENST00000706980.1:n.464+11687G>A

Variant summary

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

The ENST00000706980.1(LINC00458):​n.464+11687G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,036 control chromosomes in the GnomAD database, including 2,666 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 0.18 (2666 hom., cov: 32)
• Consequence: LINC00458 ENST00000706980.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.728
• Publications: 1 publications found

Genes affected

LINC00458 (HGNC:42807): (long intergenic non-protein coding RNA 458)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.255 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
LINC00458	ENST00000706980.1	n.464+11687G>A		intron_variant	Intron 4 of 10
LINC00458	ENST00000706981.1	n.570+54512G>A		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27746 AN: 151918 Hom.: 2656 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.183 AC: 27785 AN: 152036 Hom.: 2666 Cov.: 32 AF XY: 0.185 AC XY: 13720 AN XY: 74296

African (AFR) AF: 0.193 AC: 8004 AN: 41484

American (AMR) AF: 0.261 AC: 3984 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.140 AC: 486 AN: 3468

East Asian (EAS) AF: 0.137 AC: 708 AN: 5166

South Asian (SAS) AF: 0.205 AC: 986 AN: 4816

European-Finnish (FIN) AF: 0.173 AC: 1830 AN: 10560

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11256 AN: 67976

Other (OTH) AF: 0.181 AC: 382 AN: 2112

Alfa AF: 0.171 Hom.: 2054

Bravo AF: 0.187

Asia WGS AF: 0.197 AC: 687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.67
DANN	Benign	0.41
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs9596897; hg19: chr13-54615729;