ENST00000585627.5:n.239+46755C>T

Variant names:

• chr18-42272862-C-T
• rs898793
• ENST00000585627.5:n.239+46755C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000585627.5(LINC00907):​n.239+46755C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.789 in 151,992 control chromosomes in the GnomAD database, including 47,827 homozygotes. 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: 𝑓 0.79 (47827 hom., cov: 30)
• Consequence: LINC00907 ENST00000585627.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.783
• Publications: 1 publications found

Genes affected

LINC00907 (HGNC:44327): (long intergenic non-protein coding RNA 907)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000585627.5. 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
	LINC00907	NR_046174.2		n.402+46755C>T		intron	N/A
	LINC00907	NR_046454.1		n.402+46755C>T		intron	N/A
	LINC00907	NR_046456.1		n.403-16642C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00907	ENST00000585627.5	TSL:1	n.239+46755C>T		intron	N/A
	LINC00907	ENST00000585639.5	TSL:1	n.381+46755C>T		intron	N/A
	LINC00907	ENST00000586990.6	TSL:1	n.649+46755C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.789 AC: 119840 AN: 151874 Hom.: 47805 Cov.: 30

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.947

Gnomad AMR AF: 0.843

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.900

Gnomad FIN AF: 0.770

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.785

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

GnomAD4 genome AF: 0.789 AC: 119903 AN: 151992 Hom.: 47827 Cov.: 30 AF XY: 0.791 AC XY: 58776 AN XY: 74272

African (AFR) AF: 0.668 AC: 27680 AN: 41414

American (AMR) AF: 0.843 AC: 12870 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 2813 AN: 3472

East Asian (EAS) AF: 0.971 AC: 5006 AN: 5158

South Asian (SAS) AF: 0.901 AC: 4327 AN: 4804

European-Finnish (FIN) AF: 0.770 AC: 8145 AN: 10576

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.828 AC: 56277 AN: 67996

Other (OTH) AF: 0.787 AC: 1660 AN: 2108

Alfa AF: 0.743 Hom.: 15779

Bravo AF: 0.790

Asia WGS AF: 0.921 AC: 3202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.96
DANN	Benign	0.76
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs898793; hg19: chr18-39852827;