rs898786

chr18-42276964-G-A

Variant summary

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

The NR_046174.2(LINC00907):n.402+50857G>A 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 0.808 in 152,084 control chromosomes in the GnomAD database, including 49,819 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 0.81 (49819 hom., cov: 31)
• Consequence: LINC00907 NR_046174.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.300

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=-0.91).
• 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+50857G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00907	ENST00000589068.5	n.367+50857G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.808 AC: 122743 AN: 151966 Hom.: 49792 Cov.: 31

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.947

Gnomad AMR AF: 0.850

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.971

Gnomad SAS AF: 0.902

Gnomad FIN AF: 0.770

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.808 AC: 122817 AN: 152084 Hom.: 49819 Cov.: 31 AF XY: 0.809 AC XY: 60135 AN XY: 74322

Gnomad4 AFR AF: 0.733

Gnomad4 AMR AF: 0.850

Gnomad4 ASJ AF: 0.810

Gnomad4 EAS AF: 0.971

Gnomad4 SAS AF: 0.902

Gnomad4 FIN AF: 0.770

Gnomad4 NFE AF: 0.828

Gnomad4 OTH AF: 0.799

Alfa AF: 0.797 Hom.: 6900

Bravo AF: 0.812

Asia WGS AF: 0.923 AC: 3207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.6
Dann	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs898786; hg19: chr18-39856929;