rs2771077

Positions:

• chr9-90373882-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.261+9638C>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 0.524 in 151,510 control chromosomes in the GnomAD database, including 24,172 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 0.52 (24172 hom., cov: 32)
• Consequence: LINC01508 NR_109795.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.868

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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01508	NR_109795.1	n.261+9638C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01508	ENST00000425666.2	n.338+9638C>T		intron_variant, non_coding_transcript_variant		3
LINC01508	ENST00000436671.2	n.978+6187C>T		intron_variant, non_coding_transcript_variant		3
LINC01508	ENST00000659218.1	n.401+9638C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79337 AN: 151396 Hom.: 24116 Cov.: 32

Gnomad AFR AF: 0.858

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.594

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.524 AC: 79452 AN: 151510 Hom.: 24172 Cov.: 32 AF XY: 0.521 AC XY: 38585 AN XY: 74030

Gnomad4 AFR AF: 0.858

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.429

Gnomad4 SAS AF: 0.477

Gnomad4 FIN AF: 0.395

Gnomad4 NFE AF: 0.380

Gnomad4 OTH AF: 0.525

Alfa AF: 0.439 Hom.: 5002

Bravo AF: 0.542

Asia WGS AF: 0.491 AC: 1695 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.31
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: rs2771077; hg19: chr9-93136164;