rs906310

chr15-97761300-G-Achr15-97761300-G-Cchr15-97761300-G-T

Variant summary

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

The NR_024173.1(LINC00923):n.478-17817C>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 0.45 in 152,048 control chromosomes in the GnomAD database, including 15,788 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 0.45 (15788 hom., cov: 33)
• Consequence: LINC00923 NR_024173.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.506

Genes affected

LINC00923 (HGNC:28088): (long intergenic non-protein coding RNA 923)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00923	NR_024173.1	n.478-17817C>T		intron_variant, non_coding_transcript_variant
LINC00923	NR_024172.1	n.478-2639C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00923	ENST00000614972.4	n.689-17817C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68342 AN: 151928 Hom.: 15793 Cov.: 33

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.450 AC: 68352 AN: 152048 Hom.: 15788 Cov.: 33 AF XY: 0.456 AC XY: 33922 AN XY: 74316

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.744

Gnomad4 SAS AF: 0.559

Gnomad4 FIN AF: 0.494

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.447

Alfa AF: 0.419 Hom.: 12844

Bravo AF: 0.436

Asia WGS AF: 0.626 AC: 2176 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	6.0
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs906310; hg19: chr15-98304530;