rs10007186

Variant names:

• chr4-78667891-C-A
• rs10007186
• ENST00000778519.1:n.629C>A

Your query was ambiguous. Multiple possible variants found:

• chr4-78667891-C-A
• chr4-78667891-C-G
• chr4-78667891-C-T

Variant summary

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

The ENST00000778519.1(LINC01094):​n.629C>A 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)
• Consequence: LINC01094 ENST00000778519.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.927
• Publications: 20 publications found

Genes affected

LINC01094 (HGNC:49219): (long intergenic non-protein coding RNA 1094)

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).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000778519.1. 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
	LINC01094	NR_038303.1		n.473+4880C>A		intron	N/A
	LINC01094	NR_038304.1		n.473+4880C>A		intron	N/A
	LINC01094	NR_038305.1		n.380-5452C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01094	ENST00000778519.1		n.629C>A		non_coding_transcript_exon	Exon 4 of 4
	LINC01094	ENST00000503539.8	TSL:2	n.581+4880C>A		intron	N/A
	LINC01094	ENST00000504675.7	TSL:2	n.476+4880C>A		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 33

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.12
DANN	Benign	0.41
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs10007186; hg19: chr4-79589045;