chr2-215625044-C-A

Variant names:

• chr2-215625044-C-A
• rs2678272
• ENST00000417485.6:n.284+3119C>A

Variant summary

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

The ENST00000417485.6(ENSG00000237525):​n.284+3119C>A 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: ENSG00000237525 ENST00000417485.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.540
• Publications: 3 publications found

Genes affected

ENSG00000237525 (HGNC:):

LINC00607 (HGNC:43944): (long intergenic non-protein coding RNA 607)

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=-0.79).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000417485.6. 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
	LINC00607	NR_037195.1		n.724-809G>T		intron	N/A
	LOC102724861	NR_187734.1		n.274+3119C>A		intron	N/A
	LOC102724861	NR_187735.1		n.274+3119C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000237525	ENST00000417485.6	TSL:5	n.284+3119C>A		intron	N/A
	ENSG00000237525	ENST00000422353.6	TSL:3	n.288+3119C>A		intron	N/A
	LINC00607	ENST00000423530.5	TSL:2	n.1066-809G>T		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

Alfa AF: 0.00 Hom.: 943

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.1
DANN	Benign	0.66
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs2678272; hg19: chr2-216489767;