ENST00000425666.3:n.255-24432A>C

Variant names:

• chr9-90408153-T-G
• rs10821402
• ENST00000425666.3:n.255-24432A>C

Variant summary

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

The ENST00000425666.3(LINC01508):​n.255-24432A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.623 in 151,956 control chromosomes in the GnomAD database, including 30,364 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 0.62 (30364 hom., cov: 31)
• Consequence: LINC01508 ENST00000425666.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 0 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.73 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01508	NR_109795.1	n.60-24432A>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01508	ENST00000425666.3	n.255-24432A>C		intron_variant	Intron 1 of 2	3
LINC01508	ENST00000436671.2	n.76-22570A>C		intron_variant	Intron 1 of 4	3
LINC01508	ENST00000659218.1	n.199+19603A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.623 AC: 94631 AN: 151838 Hom.: 30352 Cov.: 31

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.836

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.704

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.623 AC: 94674 AN: 151956 Hom.: 30364 Cov.: 31 AF XY: 0.628 AC XY: 46652 AN XY: 74278

African (AFR) AF: 0.467 AC: 19338 AN: 41422

American (AMR) AF: 0.728 AC: 11114 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 2354 AN: 3470

East Asian (EAS) AF: 0.750 AC: 3871 AN: 5162

South Asian (SAS) AF: 0.650 AC: 3128 AN: 4814

European-Finnish (FIN) AF: 0.704 AC: 7422 AN: 10548

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.665 AC: 45216 AN: 67956

Other (OTH) AF: 0.623 AC: 1311 AN: 2106

Alfa AF: 0.630 Hom.: 6756

Bravo AF: 0.617

Asia WGS AF: 0.696 AC: 2421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.1
DANN	Benign	0.78
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs10821402; hg19: chr9-93170435;