rs9596897

Positions:

• chr13-54041594-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000706980.1(LINC00458):​n.464+11687G>A variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.728

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00458	ENST00000706980.1	n.464+11687G>A		intron_variant, non_coding_transcript_variant
LINC00458	ENST00000706981.1	n.570+54512G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.181

Alfa AF: 0.170 Hom.: 1183

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9596897; hg19: chr13-54615729;