15-97625256-A-G

Position:

• chr15-97625256-A-G

Variant summary

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

The ENST00000615399.1(LINC00923):​n.411+26796T>C 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 0.497 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.340

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=-0.96).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00923	ENST00000615399.1	n.411+26796T>C		intron_variant, non_coding_transcript_variant		5
LINC00923	ENST00000658023.1	n.357+26796T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.335

Gnomad4 EAS AF: 0.545

Gnomad4 SAS AF: 0.508

Gnomad4 FIN AF: 0.551

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.479

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs288421; hg19: chr15-98168486;