rs1754059

chr9-90377067-T-Achr9-90377067-T-C

Variant summary

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

The NR_109795.1(LINC01508):n.261+6453A>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 0.441 in 152,086 control chromosomes in the GnomAD database, including 15,428 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 0.44 (15428 hom., cov: 33)
• Consequence: LINC01508 NR_109795.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.182

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01508	NR_109795.1	n.261+6453A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01508	ENST00000425666.2	n.338+6453A>T		intron_variant, non_coding_transcript_variant		3
LINC01508	ENST00000436671.2	n.978+3002A>T		intron_variant, non_coding_transcript_variant		3
LINC01508	ENST00000659218.1	n.401+6453A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.441 AC: 66965 AN: 151968 Hom.: 15398 Cov.: 33

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.441 AC: 67045 AN: 152086 Hom.: 15428 Cov.: 33 AF XY: 0.441 AC XY: 32816 AN XY: 74334

Gnomad4 AFR AF: 0.565

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.431

Gnomad4 SAS AF: 0.450

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.474

Alfa AF: 0.399 Hom.: 1481

Bravo AF: 0.447

Asia WGS AF: 0.463 AC: 1613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	7.0
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1754059; hg19: chr9-93139349;