rs1021393

chr15-97864767-T-C

Variant summary

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

The NR_024173.1(LINC00923):n.477+9186A>G 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 0.352 in 151,678 control chromosomes in the GnomAD database, including 11,946 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 0.35 (11946 hom., cov: 31)
• Consequence: LINC00923 NR_024173.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.691

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00923	NR_024173.1	n.477+9186A>G		intron_variant, non_coding_transcript_variant
LINC00923	NR_024172.1	n.477+9186A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00923	ENST00000614972.4	n.598+9186A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53398 AN: 151564 Hom.: 11954 Cov.: 31

Gnomad AFR AF: 0.0856

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.352 AC: 53375 AN: 151678 Hom.: 11946 Cov.: 31 AF XY: 0.354 AC XY: 26203 AN XY: 74102

Gnomad4 AFR AF: 0.0853

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.489

Gnomad4 EAS AF: 0.194

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.581

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.389

Alfa AF: 0.446 Hom.: 7657

Bravo AF: 0.323

Asia WGS AF: 0.224 AC: 776 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.43
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1021393; hg19: chr15-98407997;