13-89833675-G-C

Variant names:

• chr13-89833675-G-C
• rs9588771
• ENST00000448259.1:n.267C>G

Variant summary

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

The ENST00000756840.1(LINC02336):​n.871G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000212 in 471,246 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 32)
  • Exomes 𝑓: 0.0000021 (0 hom.)
• Consequence: LINC02336 ENST00000756840.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296
• Publications: 1 publications found

Genes affected

RPL7L1P1 (HGNC:39455): (RPL7L1 pseudogene 1)

LINC02336 (HGNC:53256): (long intergenic non-protein coding RNA 2336)

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: ENST00000756840.1. 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
	RPL7L1P1	ENST00000448259.1	TSL:6	n.267C>G		non_coding_transcript_exon	Exon 1 of 1
	LINC02336	ENST00000756840.1		n.871G>C		non_coding_transcript_exon	Exon 5 of 5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000212 AC: 1 AN: 471246 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 255380

African (AFR) AF: 0.00 AC: 0 AN: 13524

American (AMR) AF: 0.00 AC: 0 AN: 25744

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13946

East Asian (EAS) AF: 0.00 AC: 0 AN: 31154

South Asian (SAS) AF: 0.00 AC: 0 AN: 53650

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 28640

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1856

European-Non Finnish (NFE) AF: 0.00000361 AC: 1 AN: 276922

Other (OTH) AF: 0.00 AC: 0 AN: 25810

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.81
DANN	Benign	0.54
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs9588771; hg19: chr13-90485929;