chr9-90408153-T-G

Position:

• chr9-90408153-T-G

Variant summary

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

The ENST00000425666.2(LINC01508):​n.137-24432A>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 ENST00000425666.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

Genes affected

LINC01508 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC01508	NR_109795.1	n.60-24432A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01508	ENST00000425666.2	n.137-24432A>C		intron_variant		3
LINC01508	ENST00000436671.2	n.76-22570A>C		intron_variant		3
LINC01508	ENST00000659218.1	n.199+19603A>C		intron_variant

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

Gnomad4 AFR AF: 0.467

Gnomad4 AMR AF: 0.728

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.750

Gnomad4 SAS AF: 0.650

Gnomad4 FIN AF: 0.704

Gnomad4 NFE AF: 0.665

Gnomad4 OTH AF: 0.623

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10821402; hg19: chr9-93170435;