18-10616083-T-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NR_146509.1(LINC01887):n.388+739A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 0.38 (549 hom., cov: 5)
  • Failed GnomAD Quality Control
• Consequence: LINC01887 NR_146509.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257

Genes affected

LINC01887 (HGNC:52706): (long intergenic non-protein coding RNA 1887)

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BS2: High Homozygotes in GnomAd at 548 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01887	NR_146509.1	n.388+739A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01887	ENST00000584734.1	n.310+750A>G		intron_variant, non_coding_transcript_variant		3
LINC01887	ENST00000583691.1	n.179+752A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.376 AC: 15072 AN: 40064 Hom.: 548 Cov.: 5

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.435

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.406

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.376 AC: 15065 AN: 40094 Hom.: 549 Cov.: 5 AF XY: 0.367 AC XY: 6881 AN XY: 18726

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.405

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.38
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs509049; hg19: chr18-10616080;