dbSNP rs11602954: BET1L:c.168+2755C>T (chr11-202856-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000410108.5(BET1L):c.168+2755C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 148,134 control chromosomes in the GnomAD database, including 2,511 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 0.16 ( 2502 hom., cov: 33)

Exomes 𝑓: 0.13 ( 9 hom. )

Consequence

BET1L
ENST00000410108.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.259

Publications

57 publications found

Variant links:

Genes affected

BET1L (HGNC:19348): (Bet1 golgi vesicular membrane trafficking protein like) Enables SNAP receptor activity. Involved in regulation of retrograde vesicle-mediated transport, Golgi to ER and retrograde transport, endosome to Golgi. Located in Golgi apparatus and endosome. Implicated in uterine fibroid. Biomarker of endometrial adenocarcinoma. [provided by Alliance of Genome Resources, Apr 2022]

BET1L 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=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BET1L	NM_001098787.2 link	c.*2446C>T		downstream_gene_variant		ENST00000382762.8	NP_001092257.1
BET1L	NM_016526.5 link	c.*2614C>T		downstream_gene_variant			NP_057610.2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
BET1L	ENST00000410108.5 link	c.168+2755C>T	intron_variant	Intron 3 of 5	3		ENSP00000386558.1
BET1L	ENST00000382762.8 link	c.*2446C>T	downstream_gene_variant		1	NM_001098787.2	ENSP00000372210.3
BET1L	ENST00000325147.13 link	c.*2614C>T	downstream_gene_variant		1		ENSP00000339093.7

Frequencies

GnomAD3 genomes

AF:

0.164

AC:

24131

AN:

147392

Hom.:

2501

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0647

Gnomad AMI

AF:

0.181

Gnomad AMR

AF:

0.177

Gnomad ASJ

AF:

0.113

Gnomad EAS

AF:

0.00283

Gnomad SAS

AF:

0.0866

Gnomad FIN

AF:

0.292

Gnomad MID

AF:

0.0762

Gnomad NFE

AF:

0.219

Gnomad OTH

AF:

0.160

GnomAD4 exome

AF:

0.130

AC:

AN:

608

Hom.:

AF XY:

0.131

AC XY:

AN XY:

314

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.250

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.227

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.173

AC:

AN:

358

Other (OTH)

AF:

0.100

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.164

AC:

24145

AN:

147526

Hom.:

2502

Cov.:

AF XY:

0.165

AC XY:

11918

AN XY:

72016

show subpopulations

African (AFR)

AF:

0.0646

AC:

2571

AN:

39796

American (AMR)

AF:

0.177

AC:

2638

AN:

14884

Ashkenazi Jewish (ASJ)

AF:

0.113

AC:

386

AN:

3420

East Asian (EAS)

AF:

0.00283

AC:

AN:

4592

South Asian (SAS)

AF:

0.0868

AC:

389

AN:

4484

European-Finnish (FIN)

AF:

0.292

AC:

3042

AN:

10412

Middle Eastern (MID)

AF:

0.0810

AC:

AN:

284

European-Non Finnish (NFE)

AF:

0.219

AC:

14592

AN:

66684

Other (OTH)

AF:

0.158

AC:

326

AN:

2058

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1010

2020

3029

4039

5049

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

254

508

762

1016

1270

<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:

0.185

Hom.:

8742

Bravo

AF:

0.149

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

5.3

(source)

DANN

Benign

0.82

PhyloP100

0.26

Mutation Taster

=100/0

polymorphism (auto)

(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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over