rs288423

Variant names:

• chr15-97625411-G-A
• rs288423
• ENST00000615399.1:n.411+26641C>T

Variant summary

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

The ENST00000615399.1(LINC00923):​n.411+26641C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 152,004 control chromosomes in the GnomAD database, including 19,284 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 0.50 (19284 hom., cov: 33)
• Consequence: LINC00923 ENST00000615399.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00923	ENST00000615399.1	n.411+26641C>T		intron_variant	Intron 3 of 4	5
LINC00923	ENST00000658023.1	n.357+26641C>T		intron_variant	Intron 3 of 4
LINC00923	ENST00000715390.1	n.598+26641C>T		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75396 AN: 151886 Hom.: 19254 Cov.: 33

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.497 AC: 75479 AN: 152004 Hom.: 19284 Cov.: 33 AF XY: 0.502 AC XY: 37325 AN XY: 74280

African (AFR) AF: 0.587 AC: 24341 AN: 41468

American (AMR) AF: 0.548 AC: 8372 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1165 AN: 3470

East Asian (EAS) AF: 0.545 AC: 2809 AN: 5156

South Asian (SAS) AF: 0.506 AC: 2439 AN: 4816

European-Finnish (FIN) AF: 0.552 AC: 5830 AN: 10568

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.428 AC: 29059 AN: 67940

Other (OTH) AF: 0.478 AC: 1010 AN: 2112

Alfa AF: 0.480 Hom.: 2198

Bravo AF: 0.499

Asia WGS AF: 0.546 AC: 1899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.21
DANN	Benign	0.57
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs288423; hg19: chr15-98168641;