rs898793

chr18-42272862-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_046174.2(LINC00907):n.402+46755C>T variant causes a intron, non coding transcript 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 NR_046174.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.783

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00907	NR_046174.2	n.402+46755C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00907	ENST00000589068.5	n.367+46755C>T		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.668

Gnomad4 AMR AF: 0.843

Gnomad4 ASJ AF: 0.810

Gnomad4 EAS AF: 0.971

Gnomad4 SAS AF: 0.901

Gnomad4 FIN AF: 0.770

Gnomad4 NFE AF: 0.828

Gnomad4 OTH AF: 0.787

Alfa AF: 0.695 Hom.: 8752

Bravo AF: 0.790

Asia WGS AF: 0.921 AC: 3202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.96
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs898793; hg19: chr18-39852827;