9-90304862-T-C

Variant names:

• chr9-90304862-T-C
• rs2771102
• ENST00000425666.3:n.457-3209A>G

Variant summary

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

The ENST00000425666.3(LINC01508):​n.457-3209A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 152,020 control chromosomes in the GnomAD database, including 14,298 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 0.42 (14298 hom., cov: 32)
• Consequence: LINC01508 ENST00000425666.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• Publications: 1 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01508	NR_109795.1	n.262-3209A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01508	ENST00000425666.3	n.457-3209A>G		intron_variant	Intron 2 of 2	3
LINC01508	ENST00000436671.2	n.979-3209A>G		intron_variant	Intron 4 of 4	3
LINC01508	ENST00000659218.1	n.402-3209A>G		intron_variant	Intron 2 of 2
LINC01508	ENST00000785640.1	n.485-3209A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63925 AN: 151902 Hom.: 14273 Cov.: 32

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.421 AC: 64004 AN: 152020 Hom.: 14298 Cov.: 32 AF XY: 0.422 AC XY: 31399 AN XY: 74326

African (AFR) AF: 0.554 AC: 22939 AN: 41436

American (AMR) AF: 0.417 AC: 6373 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 930 AN: 3470

East Asian (EAS) AF: 0.588 AC: 3041 AN: 5174

South Asian (SAS) AF: 0.503 AC: 2421 AN: 4812

European-Finnish (FIN) AF: 0.386 AC: 4084 AN: 10586

Middle Eastern (MID) AF: 0.339 AC: 99 AN: 292

European-Non Finnish (NFE) AF: 0.339 AC: 23022 AN: 67940

Other (OTH) AF: 0.425 AC: 897 AN: 2112

Alfa AF: 0.376 Hom.: 32848

Bravo AF: 0.429

Asia WGS AF: 0.574 AC: 1995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.2
DANN	Benign	0.73
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs2771102; hg19: chr9-93067144;