8-11762477-C-G

Variant names:

• chr8-11762477-C-G
• rs7015453
• NR_171032.1:n.1222C>G

Variant summary

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

The NR_171032.1(LINC02905):​n.1222C>G 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: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LINC02905 NR_171032.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.613
• Publications: 8 publications found

Genes affected

LINC02905 (HGNC:32200): (long intergenic non-protein coding RNA 2905)

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=-0.93).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_171032.1. 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
	LINC02905	NR_171032.1		n.1222C>G		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 39480 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 20614

African (AFR) AF: 0.00 AC: 0 AN: 1278

American (AMR) AF: 0.00 AC: 0 AN: 3534

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 784

East Asian (EAS) AF: 0.00 AC: 0 AN: 2738

South Asian (SAS) AF: 0.00 AC: 0 AN: 4924

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1246

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 138

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 22850

Other (OTH) AF: 0.00 AC: 0 AN: 1988

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.86
DANN	Benign	0.56
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs7015453; hg19: chr8-11619986;