chr7-26540630-G-C

Variant names:

• chr7-26540630-G-C
• rs1047022
• ENST00000623092.1:n.2253G>C

Variant summary

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

The ENST00000623092.1(ENSG00000280255):​n.2253G>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)
• Consequence: ENSG00000280255 ENST00000623092.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780
• Publications: 4 publications found

Genes affected

ENSG00000280255 (HGNC:):

LINC02981 (HGNC:56055): (long intergenic non-protein coding RNA 2981)

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=-0.88).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000623092.1. 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
	LINC02981	NR_148499.1		n.3763G>C		non_coding_transcript_exon	Exon 7 of 7
	LINC02981	NR_148500.1		n.3358G>C		non_coding_transcript_exon	Exon 6 of 6
	LINC02981	NR_148501.1		n.3641G>C		non_coding_transcript_exon	Exon 6 of 6

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000280255	ENST00000623092.1	TSL:6	n.2253G>C		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000301643	ENST00000780535.1		n.354-338G>C		intron	N/A
	ENSG00000301666	ENST00000780720.1		n.210-9143C>G		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 1126

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.63
DANN	Benign	0.52
PhyloP100		0.078

Splicing

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

Other links and lift over

dbSNP: rs1047022; hg19: chr7-26580249;