rs906310

Variant names:

• chr15-97761300-G-A
• rs906310
• ENST00000503768.6:n.599-2639C>T

Your query was ambiguous. Multiple possible variants found:

• chr15-97761300-G-A
• chr15-97761300-G-C
• chr15-97761300-G-T

Variant summary

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

The ENST00000503768.6(LINC00923):​n.599-2639C>T variant causes a intron 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 ENST00000503768.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.506
• Publications: 3 publications found

Genes affected

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

ENSG00000259199 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000503768.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00923	NR_024172.1		n.478-2639C>T		intron	N/A
	LINC00923	NR_024173.1		n.478-17817C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00923	ENST00000503768.6	TSL:1	n.599-2639C>T		intron	N/A
	LINC00923	ENST00000503874.3	TSL:1	n.599-17817C>T		intron	N/A
	LINC00923	ENST00000614972.4	TSL:5	n.689-17817C>T		intron	N/A

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

African (AFR) AF: 0.415 AC: 17214 AN: 41484

American (AMR) AF: 0.402 AC: 6149 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1996 AN: 3468

East Asian (EAS) AF: 0.744 AC: 3841 AN: 5162

South Asian (SAS) AF: 0.559 AC: 2692 AN: 4812

European-Finnish (FIN) AF: 0.494 AC: 5214 AN: 10554

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29723 AN: 67970

Other (OTH) AF: 0.447 AC: 945 AN: 2114

Alfa AF: 0.422 Hom.: 17172

Bravo AF: 0.436

Asia WGS AF: 0.626 AC: 2176 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.0
DANN	Benign	0.87
PhyloP100		0.51
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs906310; hg19: chr15-98304530;