15-95470914-T-C

Position:

• chr15-95470914-T-C

Variant summary

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

The NR_027132.1(LINC00924):​n.339+17041T>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 0.438 in 152,006 control chromosomes in the GnomAD database, including 15,513 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 0.44 (15513 hom., cov: 32)
• Consequence: LINC00924 NR_027132.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.834

Genes affected

LINC00924 (HGNC:27081): (long intergenic non-protein coding RNA 924)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00924	NR_027132.1	n.339+17041T>C		intron_variant, non_coding_transcript_variant
LINC00924	NR_027133.1	n.339+17041T>C		intron_variant, non_coding_transcript_variant
LOC105370993	XR_001751683.2	n.378-6105A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00924	ENST00000650234.1	n.359+17041T>C		intron_variant, non_coding_transcript_variant
	ENST00000668885.1	n.246-6105A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66468 AN: 151888 Hom.: 15501 Cov.: 32

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.438 AC: 66517 AN: 152006 Hom.: 15513 Cov.: 32 AF XY: 0.439 AC XY: 32605 AN XY: 74308

Gnomad4 AFR AF: 0.584

Gnomad4 AMR AF: 0.433

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.506

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.410

Alfa AF: 0.394 Hom.: 5648

Bravo AF: 0.437

Asia WGS AF: 0.350 AC: 1217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.5
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7170668; hg19: chr15-96014143;