18-10622047-T-G

Variant summary

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

The NR_146509.1(LINC01887):n.192+4182A>C 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 0.418 in 152,086 control chromosomes in the GnomAD database, including 13,506 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 (13506 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC01887 NR_146509.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.489

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01887	NR_146509.1	n.192+4182A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01887	ENST00000584734.1	n.125+4182A>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63528 AN: 151968 Hom.: 13492 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.418 AC: 63578 AN: 152086 Hom.: 13506 Cov.: 32 AF XY: 0.418 AC XY: 31086 AN XY: 74340

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.485

Gnomad4 ASJ AF: 0.453

Gnomad4 EAS AF: 0.467

Gnomad4 SAS AF: 0.573

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.462

Alfa AF: 0.317 Hom.: 993

Bravo AF: 0.421

Asia WGS AF: 0.546 AC: 1897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
Cadd	Benign	4.1
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10502407; hg19: chr18-10622044;