dbSNP rs749924: LINC01880:n.-206G>A (chr2-242084344-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000446593.1(LINC01880):n.-206G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 148,494 control chromosomes in the GnomAD database, including 5,334 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 0.25 ( 5334 hom., cov: 30)

Consequence

LINC01880
ENST00000446593.1 upstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.49

Variant links:

Genes affected

LINC01880 (HGNC:52699): (long intergenic non-protein coding RNA 1880)

LINC01880 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01880	NR_146651.1 link	n.-206G>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
LINC01880	ENST00000446593.1 link	n.-206G>A	upstream_gene_variant	4
LINC01880	ENST00000661866.1 link	n.-111G>A	upstream_gene_variant
LINC01880	ENST00000662783.1 link	n.-213G>A	upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.253

AC:

37515

AN:

148380

Hom.:

5314

Cov.:

show subpopulations

Gnomad AFR

AF:

0.447

Gnomad AMI

AF:

0.156

Gnomad AMR

AF:

0.347

Gnomad ASJ

AF:

0.161

Gnomad EAS

AF:

0.435

Gnomad SAS

AF:

0.348

Gnomad FIN

AF:

0.174

Gnomad MID

AF:

0.215

Gnomad NFE

AF:

0.117

Gnomad OTH

AF:

0.241

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

GnomAD4 genome

AF:

0.253

AC:

37582

AN:

148494

Hom.:

5334

Cov.:

AF XY:

0.259

AC XY:

18770

AN XY:

72484

show subpopulations

Gnomad4 AFR

AF:

0.447

Gnomad4 AMR

AF:

0.348

Gnomad4 ASJ

AF:

0.161

Gnomad4 EAS

AF:

0.434

Gnomad4 SAS

AF:

0.346

Gnomad4 FIN

AF:

0.174

Gnomad4 NFE

AF:

0.117

Gnomad4 OTH

AF:

0.246

Alfa

AF:

0.208

Hom.:

482

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.69

DANN

Benign

0.63

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over