rs883924

Variant names:

• chr9-90419249-G-A
• rs883924
• ENST00000425666.3:n.254+14182C>T

Variant summary

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

The ENST00000425666.3(LINC01508):​n.254+14182C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 151,866 control chromosomes in the GnomAD database, including 9,780 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 0.32 (9780 hom., cov: 31)
• Consequence: LINC01508 ENST00000425666.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296
• Publications: 6 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01508	NR_109795.1	n.59+14182C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01508	ENST00000425666.3	n.254+14182C>T		intron_variant	Intron 1 of 2	3
LINC01508	ENST00000436671.2	n.75+14182C>T		intron_variant	Intron 1 of 4	3
LINC01508	ENST00000659218.1	n.199+8507C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48561 AN: 151748 Hom.: 9753 Cov.: 31

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.320 AC: 48641 AN: 151866 Hom.: 9780 Cov.: 31 AF XY: 0.316 AC XY: 23473 AN XY: 74216

African (AFR) AF: 0.571 AC: 23612 AN: 41346

American (AMR) AF: 0.303 AC: 4632 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 929 AN: 3472

East Asian (EAS) AF: 0.234 AC: 1210 AN: 5160

South Asian (SAS) AF: 0.163 AC: 781 AN: 4800

European-Finnish (FIN) AF: 0.205 AC: 2163 AN: 10542

Middle Eastern (MID) AF: 0.384 AC: 112 AN: 292

European-Non Finnish (NFE) AF: 0.212 AC: 14377 AN: 67962

Other (OTH) AF: 0.317 AC: 669 AN: 2112

Alfa AF: 0.252 Hom.: 4561

Bravo AF: 0.340

Asia WGS AF: 0.230 AC: 799 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	0.69
DANN	Benign	0.33
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs883924; hg19: chr9-93181531;