Variant rs977785 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_026970.1(LY86-AS1):n.196-19159T>G 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 0.727 in 1,483,312 control chromosomes in the GnomAD database, including 392,704 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 0.71 ( 38176 hom., cov: 33)

Exomes 𝑓: 0.73 ( 354528 hom. )

Consequence

LY86-AS1
NR_026970.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0680

Variant links:

Genes affected

LY86-AS1 (HGNC:26593): (LY86 antisense RNA 1)

LY86-AS1 links:

LY86 (HGNC:16837): (lymphocyte antigen 86) Acts upstream of or within positive regulation of lipopolysaccharide-mediated signaling pathway. Predicted to be located in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

LY86 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LY86-AS1	NR_026970.1 linkuse as main transcript	n.196-19159T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LY86-AS1	ENST00000429345.5 linkuse as main transcript	n.114-19159T>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.708

AC:

107659

AN:

152062

Hom.:

38163

Cov.:

show subpopulations

Gnomad AFR

AF:

0.651

Gnomad AMI

AF:

0.589

Gnomad AMR

AF:

0.713

Gnomad ASJ

AF:

0.768

Gnomad EAS

AF:

0.660

Gnomad SAS

AF:

0.739

Gnomad FIN

AF:

0.751

Gnomad MID

AF:

0.728

Gnomad NFE

AF:

0.735

Gnomad OTH

AF:

0.703

GnomAD4 exome

AF:

0.729

AC:

970839

AN:

1331132

Hom.:

354528

Cov.:

AF XY:

0.731

AC XY:

481575

AN XY:

658402

show subpopulations

Gnomad4 AFR exome

AF:

0.652

Gnomad4 AMR exome

AF:

0.731

Gnomad4 ASJ exome

AF:

0.775

Gnomad4 EAS exome

AF:

0.672

Gnomad4 SAS exome

AF:

0.749

Gnomad4 FIN exome

AF:

0.741

Gnomad4 NFE exome

AF:

0.730

Gnomad4 OTH exome

AF:

0.732

GnomAD4 genome

AF:

0.708

AC:

107706

AN:

152180

Hom.:

38176

Cov.:

AF XY:

0.707

AC XY:

52576

AN XY:

74408

show subpopulations

Gnomad4 AFR

AF:

0.651

Gnomad4 AMR

AF:

0.713

Gnomad4 ASJ

AF:

0.768

Gnomad4 EAS

AF:

0.660

Gnomad4 SAS

AF:

0.739

Gnomad4 FIN

AF:

0.751

Gnomad4 NFE

AF:

0.735

Gnomad4 OTH

AF:

0.697

Alfa

AF:

0.732

Hom.:

82706

Bravo

AF:

0.704

Asia WGS

AF:

0.655

AC:

2278

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

5.5

DANN

Benign

0.74

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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