rs9596905

Positions:

• chr13-54059238-G-A
• chr13-54059238-G-T

Variant summary

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

The ENST00000706980.1(LINC00458):​n.341-5834C>T 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 0.132 in 151,790 control chromosomes in the GnomAD database, including 2,253 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 0.13 (2253 hom., cov: 32)
• Consequence: LINC00458 ENST00000706980.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00458	ENST00000706980.1	n.341-5834C>T		intron_variant, non_coding_transcript_variant
LINC00458	ENST00000706981.1	n.570+36868C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20030 AN: 151670 Hom.: 2248 Cov.: 32

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.0799

Gnomad ASJ AF: 0.0575

Gnomad EAS AF: 0.0789

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0368

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0626

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.132 AC: 20039 AN: 151790 Hom.: 2253 Cov.: 32 AF XY: 0.130 AC XY: 9637 AN XY: 74182

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.0798

Gnomad4 ASJ AF: 0.0575

Gnomad4 EAS AF: 0.0789

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.0368

Gnomad4 NFE AF: 0.0626

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0798 Hom.: 309

Bravo AF: 0.141

Asia WGS AF: 0.0960 AC: 333 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.43
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9596905; hg19: chr13-54633373;