Genetic Variant 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000410108.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BET1L	NM_001098787.2	MANE Select	c.*2446C>T		downstream_gene	N/A	NP_001092257.1
	BET1L	NM_016526.5		c.*2614C>T		downstream_gene	N/A	NP_057610.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
BET1L	ENST00000410108.5	TSL:3	c.168+2755C>T	intron	N/A	ENSP00000386558.1
BET1L	ENST00000382762.8	TSL:1 MANE Select	c.*2446C>T	downstream_gene	N/A	ENSP00000372210.3
BET1L	ENST00000325147.13	TSL:1	c.*2614C>T	downstream_gene	N/A	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 v4.9

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over