chr15-97864767-T-C

Variant names:

• chr15-97864767-T-C
• rs1021393
• ENST00000503768.6:n.598+9186A>G

Variant summary

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

The ENST00000503768.6(LINC00923):​n.598+9186A>G variant causes a intron 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 ENST00000503768.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.691
• Publications: 2 publications found

Genes affected

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

ENSG00000259199 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC00923	NR_024172.1	n.477+9186A>G		intron_variant	Intron 1 of 2
LINC00923	NR_024173.1	n.477+9186A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00923	ENST00000503768.6	n.598+9186A>G		intron_variant	Intron 1 of 2	1
LINC00923	ENST00000503874.3	n.598+9186A>G		intron_variant	Intron 1 of 1	1
LINC00923	ENST00000558179.1	n.53+9186A>G		intron_variant	Intron 1 of 1	3

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

African (AFR) AF: 0.0853 AC: 3536 AN: 41436

American (AMR) AF: 0.338 AC: 5142 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1696 AN: 3468

East Asian (EAS) AF: 0.194 AC: 997 AN: 5130

South Asian (SAS) AF: 0.282 AC: 1354 AN: 4802

European-Finnish (FIN) AF: 0.581 AC: 6062 AN: 10440

Middle Eastern (MID) AF: 0.455 AC: 133 AN: 292

European-Non Finnish (NFE) AF: 0.488 AC: 33133 AN: 67870

Other (OTH) AF: 0.389 AC: 821 AN: 2112

Alfa AF: 0.448 Hom.: 8515

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
PhyloP100		-0.69
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1021393; hg19: chr15-98407997;