15-95470914-T-C

Variant names:

• chr15-95470914-T-C
• rs7170668
• ENST00000554837.5:n.337+17041T>C

Variant summary

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

The ENST00000554837.5(LINC00924):​n.337+17041T>C variant causes a intron 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 ENST00000554837.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.834
• Publications: 7 publications found

Genes affected

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

ENSG00000258489 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000554837.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00924	NR_027132.1		n.339+17041T>C		intron	N/A
	LINC00924	NR_027133.1		n.339+17041T>C		intron	N/A
	LOC105370993	NR_188325.1		n.186-6105A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00924	ENST00000554837.5	TSL:1	n.337+17041T>C		intron	N/A
	ENSG00000258489	ENST00000554412.3	TSL:2	n.131-6105A>G		intron	N/A
	LINC00924	ENST00000556053.2	TSL:2	n.337+17041T>C		intron	N/A

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

African (AFR) AF: 0.584 AC: 24197 AN: 41454

American (AMR) AF: 0.433 AC: 6613 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1332 AN: 3468

East Asian (EAS) AF: 0.202 AC: 1043 AN: 5172

South Asian (SAS) AF: 0.506 AC: 2436 AN: 4818

European-Finnish (FIN) AF: 0.426 AC: 4496 AN: 10550

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.370 AC: 25125 AN: 67956

Other (OTH) AF: 0.410 AC: 866 AN: 2114

Alfa AF: 0.387 Hom.: 20624

Bravo AF: 0.437

Asia WGS AF: 0.350 AC: 1217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.5
DANN	Benign	0.82
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs7170668; hg19: chr15-96014143;