rs11082277

Positions:

• chr18-42470398-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.872+15409G>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 0.42 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 NR_046174.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939

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=-0.83).
• 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/exons	MANE	UniProt
LINC00907	NR_046174.2	n.872+15409G>A		intron_variant, non_coding_transcript_variant
LINC00907	NR_046454.1	n.652+15409G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00907	ENST00000585627.5	n.489+15409G>A		intron_variant, non_coding_transcript_variant		1
LINC00907	ENST00000585639.5	n.631+15409G>A		intron_variant, non_coding_transcript_variant		1
LINC00907	ENST00000589068.5	n.837+15409G>A		intron_variant, non_coding_transcript_variant		2
LINC00907	ENST00000591381.5	n.472+15409G>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.477

Gnomad4 ASJ AF: 0.596

Gnomad4 EAS AF: 0.117

Gnomad4 SAS AF: 0.586

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.576

Gnomad4 OTH AF: 0.446

Alfa AF: 0.547 Hom.: 31437

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11082277; hg19: chr18-40050363;