ENST00000450977.2:n.240-734A>C

Variant names:

• chr7-84570245-A-C
• rs722453
• ENST00000450977.2:n.240-734A>C

Variant summary

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

The ENST00000450977.2(LINC03017):​n.240-734A>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: LINC03017 ENST00000450977.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193
• Publications: 1 publications found

Genes affected

LINC03017 (HGNC:56146): (long intergenic non-protein coding RNA 3017)

ENSG00000301054 (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=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03017	NR_110079.1	n.240-734A>C		intron_variant	Intron 2 of 2
LINC03017	NR_110080.1	n.240-734A>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03017	ENST00000450977.2	n.240-734A>C		intron_variant	Intron 2 of 2	1
LINC03017	ENST00000446000.2	n.190-734A>C		intron_variant	Intron 2 of 3	3
ENSG00000301054	ENST00000775795.1	n.139-4156T>G		intron_variant	Intron 2 of 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	1.5
DANN	Benign	0.38
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs722453; hg19: chr7-84199561;