15-97625256-A-G

Variant names:

• chr15-97625256-A-G
• rs288421
• ENST00000615399.1:n.411+26796T>C

Variant summary

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

The ENST00000615399.1(LINC00923):​n.411+26796T>C 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 152,030 control chromosomes in the GnomAD database, including 19,318 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 (19318 hom., cov: 33)
• Consequence: LINC00923 ENST00000615399.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.340
• Publications: 0 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.58 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+26796T>C		intron_variant	Intron 3 of 4	5
LINC00923	ENST00000658023.1	n.357+26796T>C		intron_variant	Intron 3 of 4
LINC00923	ENST00000715390.1	n.598+26796T>C		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75482 AN: 151912 Hom.: 19288 Cov.: 33

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.497 AC: 75565 AN: 152030 Hom.: 19318 Cov.: 33 AF XY: 0.503 AC XY: 37369 AN XY: 74304

African (AFR) AF: 0.586 AC: 24305 AN: 41456

American (AMR) AF: 0.549 AC: 8387 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1161 AN: 3464

East Asian (EAS) AF: 0.545 AC: 2814 AN: 5164

South Asian (SAS) AF: 0.508 AC: 2450 AN: 4822

European-Finnish (FIN) AF: 0.551 AC: 5812 AN: 10550

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

European-Non Finnish (NFE) AF: 0.429 AC: 29173 AN: 67976

Other (OTH) AF: 0.479 AC: 1011 AN: 2110

Alfa AF: 0.473 Hom.: 2074

Bravo AF: 0.500

Asia WGS AF: 0.547 AC: 1901 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.0
DANN	Benign	0.57
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs288421; hg19: chr15-98168486;