9-90429657-T-C

Variant names:

• chr9-90429657-T-C
• rs9332454
• ENST00000425666.3:n.254+3774A>G

Variant summary

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

The ENST00000425666.3(LINC01508):​n.254+3774A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 152,024 control chromosomes in the GnomAD database, including 18,135 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 0.45 (18135 hom., cov: 32)
• Consequence: LINC01508 ENST00000425666.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0680
• Publications: 3 publications found

Genes affected

LINC01508 (HGNC:51190): (long intergenic non-protein coding RNA 1508)

ENSG00000302334 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01508	NR_109795.1	n.59+3774A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01508	ENST00000425666.3	n.254+3774A>G		intron_variant	Intron 1 of 2	3
LINC01508	ENST00000436671.2	n.75+3774A>G		intron_variant	Intron 1 of 4	3
LINC01508	ENST00000785640.1	n.110+3774A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68794 AN: 151904 Hom.: 18139 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.453 AC: 68796 AN: 152024 Hom.: 18135 Cov.: 32 AF XY: 0.455 AC XY: 33808 AN XY: 74314

African (AFR) AF: 0.162 AC: 6719 AN: 41458

American (AMR) AF: 0.540 AC: 8254 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1783 AN: 3472

East Asian (EAS) AF: 0.586 AC: 3025 AN: 5160

South Asian (SAS) AF: 0.463 AC: 2230 AN: 4816

European-Finnish (FIN) AF: 0.559 AC: 5903 AN: 10552

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.576 AC: 39173 AN: 67972

Other (OTH) AF: 0.441 AC: 931 AN: 2110

Alfa AF: 0.421 Hom.: 2163

Bravo AF: 0.439

Asia WGS AF: 0.494 AC: 1716 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	1.9
DANN	Benign	0.61
PhyloP100		0.068

Splicing

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

Other links and lift over

dbSNP: rs9332454; hg19: chr9-93191939;