rs11082277

Variant names:

• chr18-42470398-G-A
• rs11082277
• ENST00000585627.5:n.489+15409G>A

Variant summary

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

The ENST00000585627.5(LINC00907):​n.489+15409G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 151,906 control chromosomes in the GnomAD database, including 16,796 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 0.42 (16796 hom., cov: 31)
• Consequence: LINC00907 ENST00000585627.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939
• Publications: 5 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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00907	NR_046174.2	n.872+15409G>A		intron_variant	Intron 6 of 9
LINC00907	NR_046454.1	n.652+15409G>A		intron_variant	Intron 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00907	ENST00000585627.5	n.489+15409G>A		intron_variant	Intron 4 of 4	1
LINC00907	ENST00000585639.5	n.631+15409G>A		intron_variant	Intron 5 of 6	1
LINC00907	ENST00000591381.5	n.472+15409G>A		intron_variant	Intron 4 of 4	1

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63762 AN: 151788 Hom.: 16790 Cov.: 31

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.420 AC: 63771 AN: 151906 Hom.: 16796 Cov.: 31 AF XY: 0.419 AC XY: 31076 AN XY: 74184

African (AFR) AF: 0.108 AC: 4488 AN: 41462

American (AMR) AF: 0.477 AC: 7280 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.596 AC: 2063 AN: 3464

East Asian (EAS) AF: 0.117 AC: 605 AN: 5156

South Asian (SAS) AF: 0.586 AC: 2814 AN: 4798

European-Finnish (FIN) AF: 0.543 AC: 5705 AN: 10516

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.576 AC: 39136 AN: 67940

Other (OTH) AF: 0.446 AC: 943 AN: 2114

Alfa AF: 0.506 Hom.: 41252

Bravo AF: 0.397

Asia WGS AF: 0.338 AC: 1178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.5
DANN	Benign	0.82
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs11082277; hg19: chr18-40050363;