dbSNP rs10487243: BET1-AS1:n.75+18310A>G (chr7-94041217-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000415536.5(BET1-AS1):n.75+18310A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,212 control chromosomes in the GnomAD database, including 4,321 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 0.14 ( 4321 hom., cov: 32)

Consequence

BET1-AS1
ENST00000415536.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.307

Publications

3 publications found

Variant links:

Genes affected

BET1-AS1 (HGNC:40690): (BET1 antisense RNA 1)

BET1-AS1 links:

LOC130890646 (HGNC:):

LOC130890646 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=-0.81).

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
LOC130890646	NR_186703.1 link	n.102+18310A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
BET1-AS1	ENST00000415536.5 link	n.75+18310A>G	intron_variant	Intron 1 of 3	3
BET1-AS1	ENST00000718187.1 link	n.347-20239A>G	intron_variant	Intron 3 of 6
BET1-AS1	ENST00000718188.1 link	n.379-18579A>G	intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.141

AC:

21441

AN:

152094

Hom.:

4315

Cov.:

show subpopulations

Gnomad AFR

AF:

0.448

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0691

Gnomad ASJ

AF:

0.0294

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00642

Gnomad FIN

AF:

0.00904

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.0208

Gnomad OTH

AF:

0.101

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

GnomAD4 genome

AF:

0.141

AC:

21473

AN:

152212

Hom.:

4321

Cov.:

AF XY:

0.136

AC XY:

10103

AN XY:

74440

show subpopulations

African (AFR)

AF:

0.447

AC:

18545

AN:

41484

American (AMR)

AF:

0.0690

AC:

1055

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0294

AC:

102

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5186

South Asian (SAS)

AF:

0.00601

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.00904

AC:

AN:

10620

Middle Eastern (MID)

AF:

0.0680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0208

AC:

1413

AN:

68020

Other (OTH)

AF:

0.101

AC:

212

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

666

1331

1997

2662

3328

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

182

364

546

728

910

<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:

0.0501

Hom.:

1331

Bravo

AF:

0.160

Asia WGS

AF:

0.0290

AC:

100

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

5.9

(source)

DANN

Benign

0.75

PhyloP100

0.31

Mutation Taster

=100/0

polymorphism

(source)

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