chr20-18381653-C-T

Variant names:

• chr20-18381653-C-T
• rs2328293
• ENST00000423033.1:n.*169C>T

Variant summary

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

The ENST00000423033.1(LINC00851):​n.*169C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.803 in 152,078 control chromosomes in the GnomAD database, including 49,777 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 0.80 (49777 hom., cov: 30)
• Consequence: LINC00851 ENST00000423033.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91

Genes affected

LINC00851 (HGNC:43424): (long intergenic non-protein coding RNA 851)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00851	NR_034167.1	n.*169C>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00851	ENST00000423033.1	n.*169C>T		downstream_gene_variant		1
LINC00851	ENST00000594642.1	n.*172C>T		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.803 AC: 122024 AN: 151958 Hom.: 49761 Cov.: 30

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.859

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.899

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.869

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.803 AC: 122076 AN: 152078 Hom.: 49777 Cov.: 30 AF XY: 0.806 AC XY: 59913 AN XY: 74362

Gnomad4 AFR AF: 0.639

Gnomad4 AMR AF: 0.832

Gnomad4 ASJ AF: 0.859

Gnomad4 EAS AF: 0.873

Gnomad4 SAS AF: 0.837

Gnomad4 FIN AF: 0.899

Gnomad4 NFE AF: 0.869

Gnomad4 OTH AF: 0.793

Alfa AF: 0.848 Hom.: 25008

Bravo AF: 0.786

Asia WGS AF: 0.814 AC: 2834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.34
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2328293; hg19: chr20-18362297;