chr15-93825268-G-T

Variant names:

• chr15-93825268-G-T
• rs6416595
• ENST00000553818.1:n.195+3712C>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000553818.1(LINC01579):​n.195+3712C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0000081 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LINC01579 ENST00000553818.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98
• Publications: 1 publications found

Genes affected

LINC01579 (HGNC:27519): (long intergenic non-protein coding RNA 1579)

ENSG00000258627 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000553818.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01579	ENST00000553818.1	TSL:4	n.195+3712C>A		intron	N/A
	LINC01579	ENST00000557481.6	TSL:5	n.431-4168C>A		intron	N/A
	LINC01579	ENST00000766606.1		n.724-4168C>A		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000814 AC: 2 AN: 245748 Hom.: 0 AF XY: 0.0000141 AC XY: 2 AN XY: 142120

African (AFR) AF: 0.00 AC: 0 AN: 5384

American (AMR) AF: 0.00 AC: 0 AN: 15050

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 5742

East Asian (EAS) AF: 0.00 AC: 0 AN: 9086

South Asian (SAS) AF: 0.0000242 AC: 1 AN: 41330

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 17324

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 934

European-Non Finnish (NFE) AF: 0.00000717 AC: 1 AN: 139494

Other (OTH) AF: 0.00 AC: 0 AN: 11404

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 1276

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.60
DANN	Benign	0.37
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs6416595; hg19: chr15-94368497;