Variant 13-78806681-T-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_046869.2(LINC00331):n.225-14379A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 151,746 control chromosomes in the GnomAD database, including 8,384 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 0.32 ( 8384 hom., cov: 31)

Consequence

LINC00331
NR_046869.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.212

Variant links:

Genes affected

LINC00331 (HGNC:42048): (long intergenic non-protein coding RNA 331)

LINC00331 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=-0.97).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00331	NR_046869.2 link	n.225-14379A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect
LINC00331	ENST00000653901.1 link	n.112-14189A>C	intron_variant
LINC00331	ENST00000655539.1 link	n.225-14379A>C	intron_variant
LINC00331	ENST00000658469.1 link	n.225-10582A>C	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.319

AC:

48442

AN:

151628

Hom.:

8379

Cov.:

show subpopulations

Gnomad AFR

AF:

0.205

Gnomad AMI

AF:

0.260

Gnomad AMR

AF:

0.446

Gnomad ASJ

AF:

0.379

Gnomad EAS

AF:

0.477

Gnomad SAS

AF:

0.355

Gnomad FIN

AF:

0.268

Gnomad MID

AF:

0.417

Gnomad NFE

AF:

0.350

Gnomad OTH

AF:

0.351

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

GnomAD4 genome

AF:

0.319

AC:

48462

AN:

151746

Hom.:

8384

Cov.:

AF XY:

0.320

AC XY:

23755

AN XY:

74150

show subpopulations

Gnomad4 AFR

AF:

0.205

Gnomad4 AMR

AF:

0.446

Gnomad4 ASJ

AF:

0.379

Gnomad4 EAS

AF:

0.475

Gnomad4 SAS

AF:

0.354

Gnomad4 FIN

AF:

0.268

Gnomad4 NFE

AF:

0.350

Gnomad4 OTH

AF:

0.354

Alfa

AF:

0.351

Hom.:

2516

Bravo

AF:

0.331

Asia WGS

AF:

0.413

AC:

1430

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

6.3

DANN

Benign

0.59

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