9-129495504-C-G

Variant names:

• chr9-129495504-C-G
• rs1220789
• ENST00000412141.2:n.203+1909C>G

Variant summary

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

The ENST00000412141.2(LINC00963):​n.203+1909C>G 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: 33)
• Consequence: LINC00963 ENST00000412141.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84
• Publications: 7 publications found

Genes affected

LINC00963 (HGNC:48716): (long intergenic non-protein coding RNA 963)

ENSG00000309757 (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=-0.81).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00963	NR_038955.1	n.758+1909C>G		intron_variant	Intron 2 of 4
LOC124900275	XM_047424322.1	c.*222+1909C>G		intron_variant	Intron 2 of 2		XP_047280278.1
LOC124900275	XM_047424323.1	c.*225+1909C>G		intron_variant	Intron 2 of 2		XP_047280279.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00963	ENST00000412141.2	n.203+1909C>G		intron_variant	Intron 2 of 4	1
LINC00963	ENST00000419300.3	n.200+6205C>G		intron_variant	Intron 1 of 1	1
LINC00963	ENST00000444184.7	n.935+1909C>G		intron_variant	Intron 2 of 2	1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.72
DANN	Benign	0.49
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1220789; hg19: chr9-132257783;