7-25786929-C-G

Variant names:

• chr7-25786929-C-G
• rs6943606
• ENST00000812174.1:n.297+61997G>C

Variant summary

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

The ENST00000812174.1(ENSG00000286725):​n.297+61997G>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: 33)
• Consequence: ENSG00000286725 ENST00000812174.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.325
• Publications: 5 publications found

Genes affected

ENSG00000286725 (HGNC:):

LINC03007 (HGNC:56132): (long intergenic non-protein coding RNA 3007)

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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03007	NR_157808.1	n.367+2824G>C		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286725	ENST00000812174.1	n.297+61997G>C		intron_variant	Intron 2 of 4
ENSG00000286725	ENST00000812175.1	n.280+61997G>C		intron_variant	Intron 2 of 5
ENSG00000286725	ENST00000812176.1	n.297+61997G>C		intron_variant	Intron 2 of 4
ENSG00000286725	ENST00000812177.1	n.280+61997G>C		intron_variant	Intron 2 of 2

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.: 254

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.3
DANN	Benign	0.44
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs6943606; hg19: chr7-25826549;