rs9596905

Variant names:

• chr13-54059238-G-A
• rs9596905
• ENST00000706980.1:n.341-5834C>T

Your query was ambiguous. Multiple possible variants found:

• 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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00458	ENST00000706980.1	n.341-5834C>T		intron_variant	Intron 3 of 10
LINC00458	ENST00000706981.1	n.570+36868C>T		intron_variant	Intron 5 of 5

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;