rs883924

Positions:

• chr9-90419249-G-A

Variant summary

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

The NR_109795.1(LINC01508):​n.59+14182C>T variant causes a intron, non coding transcript 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 NR_109795.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC01508	NR_109795.1	n.59+14182C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01508	ENST00000425666.2	n.136+14182C>T		intron_variant, non_coding_transcript_variant		3
LINC01508	ENST00000436671.2	n.75+14182C>T		intron_variant, non_coding_transcript_variant		3
LINC01508	ENST00000659218.1	n.199+8507C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.571

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.234

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.317

Alfa AF: 0.242 Hom.: 2650

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs883924; hg19: chr9-93181531;