dbSNP rs10485086: LY86-AS1:n.279+9607A>G (chr6-6554688-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000429345.5(LY86-AS1):n.279+9607A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0847 in 152,230 control chromosomes in the GnomAD database, including 1,073 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 0.085 ( 1073 hom., cov: 33)

Consequence

LY86-AS1
ENST00000429345.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.71

Publications

1 publications found

Variant links:

Genes affected

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

LY86-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LY86-AS1	NR_026970.1 link	n.361+9607A>G		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LY86-AS1	ENST00000429345.5 link	n.279+9607A>G	intron_variant	Intron 3 of 7	2
LY86-AS1	ENST00000435641.5 link	n.482+9607A>G	intron_variant	Intron 3 of 6	2
LY86-AS1	ENST00000447858.1 link	n.149+32357A>G	intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes

AF:

0.0846

AC:

12874

AN:

152112

Hom.:

1075

Cov.:

show subpopulations

Gnomad AFR

AF:

0.196

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0804

Gnomad ASJ

AF:

0.00691

Gnomad EAS

AF:

0.254

Gnomad SAS

AF:

0.0228

Gnomad FIN

AF:

0.0686

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0179

Gnomad OTH

AF:

0.0637

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

GnomAD4 genome

AF:

0.0847

AC:

12888

AN:

152230

Hom.:

1073

Cov.:

AF XY:

0.0884

AC XY:

6582

AN XY:

74446

show subpopulations

African (AFR)

AF:

0.196

AC:

8122

AN:

41508

American (AMR)

AF:

0.0805

AC:

1232

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.00691

AC:

AN:

3472

East Asian (EAS)

AF:

0.253

AC:

1309

AN:

5174

South Asian (SAS)

AF:

0.0232

AC:

112

AN:

4830

European-Finnish (FIN)

AF:

0.0686

AC:

727

AN:

10604

Middle Eastern (MID)

AF:

0.0408

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0179

AC:

1218

AN:

68026

Other (OTH)

AF:

0.0626

AC:

132

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

557

1115

1672

2230

2787

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

132

264

396

528

660

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0353

Hom.:

456

Bravo

AF:

0.0922

Asia WGS

AF:

0.118

AC:

411

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.095

(source)

DANN

Benign

0.54

PhyloP100

-1.7

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over