6-169158234-A-G

Variant names:

• chr6-169158234-A-G
• rs10485333
• ENST00000439703.1:n.505T>C

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The ENST00000439703.1(LINC01615):​n.505T>C variant causes a non coding transcript exon 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: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LINC01615 ENST00000439703.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.53
• Publications: 3 publications found

Genes affected

LINC01615 (HGNC:51898): (long intergenic non-protein coding RNA 1615)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000439703.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01615	NR_132622.1		n.630T>C		non_coding_transcript_exon	Exon 4 of 4
	LINC01615	NR_132623.1		n.570T>C		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01615	ENST00000439703.1	TSL:2	n.505T>C		non_coding_transcript_exon	Exon 2 of 2
	LINC01615	ENST00000634877.2	TSL:5	n.735T>C		non_coding_transcript_exon	Exon 3 of 3
	LINC01615	ENST00000651190.1		n.561T>C		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 234834 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 118450

African (AFR) AF: 0.00 AC: 0 AN: 6884

American (AMR) AF: 0.00 AC: 0 AN: 6922

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 8736

East Asian (EAS) AF: 0.00 AC: 0 AN: 22574

South Asian (SAS) AF: 0.00 AC: 0 AN: 2918

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 20186

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1208

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 149828

Other (OTH) AF: 0.00 AC: 0 AN: 15578

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 2

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	12
DANN	Benign	0.88
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs10485333; hg19: chr6-169558329;