rs898786

Variant names:

• chr18-42276964-G-A
• rs898786
• ENST00000585627.5:n.239+50857G>A

Variant summary

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

The ENST00000585627.5(LINC00907):​n.239+50857G>A variant causes a intron 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 ENST00000585627.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.300
• 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=-0.91).
• 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 rank	MANE	Protein	UniProt
LINC00907	NR_046174.2	n.402+50857G>A		intron_variant	Intron 3 of 9
LINC00907	NR_046454.1	n.402+50857G>A		intron_variant	Intron 3 of 6
LINC00907	NR_046456.1	n.403-12540G>A		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00907	ENST00000585627.5	n.239+50857G>A		intron_variant	Intron 2 of 4	1
LINC00907	ENST00000585639.5	n.381+50857G>A		intron_variant	Intron 3 of 6	1
LINC00907	ENST00000586990.6	n.649+50857G>A		intron_variant	Intron 3 of 4	1

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

African (AFR) AF: 0.733 AC: 30380 AN: 41450

American (AMR) AF: 0.850 AC: 12980 AN: 15276

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

East Asian (EAS) AF: 0.971 AC: 5028 AN: 5180

South Asian (SAS) AF: 0.902 AC: 4349 AN: 4822

European-Finnish (FIN) AF: 0.770 AC: 8144 AN: 10572

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.828 AC: 56312 AN: 67994

Other (OTH) AF: 0.799 AC: 1687 AN: 2112

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
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs898786; hg19: chr18-39856929;