rs288423

Positions:

• chr15-97625411-G-A

Variant summary

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

The ENST00000615399.1(LINC00923):​n.411+26641C>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 0.497 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143

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=-0.97).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00923	ENST00000615399.1	n.411+26641C>T		intron_variant, non_coding_transcript_variant		5
LINC00923	ENST00000658023.1	n.357+26641C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.587

Gnomad4 AMR AF: 0.548

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.545

Gnomad4 SAS AF: 0.506

Gnomad4 FIN AF: 0.552

Gnomad4 NFE AF: 0.428

Gnomad4 OTH AF: 0.478

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs288423; hg19: chr15-98168641;