ENST00000417485.6:n.987-260G>C

Variant names:

• chr2-215712980-G-C
• rs10498043
• ENST00000417485.6:n.987-260G>C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000417485.6(ENSG00000237525):​n.987-260G>C 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: 31)
• Consequence: ENSG00000237525 ENST00000417485.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.414

Genes affected

ENSG00000237525 (HGNC:):

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

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00607	NR_037195.1	n.723+27897C>G		intron_variant	Intron 5 of 9
LOC102724861	NR_187736.1	n.623-260G>C		intron_variant	Intron 4 of 4
LOC102724861	NR_187737.1	n.1005-260G>C		intron_variant	Intron 7 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000237525	ENST00000417485.6	n.987-260G>C		intron_variant	Intron 7 of 7	5
LINC00607	ENST00000417922.2	n.511-11761C>G		intron_variant	Intron 4 of 5	4
LINC00607	ENST00000423530.5	n.476+30834C>G		intron_variant	Intron 4 of 8	2

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.2
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498043; hg19: chr2-216577703;