Genetic Variant BET1L:c.*1240A>G (chr11-204062-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 NM_001098787.2(BET1L):c.*1240A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.689 in 152,726 control chromosomes in the GnomAD database, including 37,660 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 0.69 ( 37483 hom., cov: 33)

Exomes 𝑓: 0.76 ( 177 hom. )

Consequence

BET1L
NM_001098787.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.80

Publications

14 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:

ENSG00000254559 (HGNC:):

ENSG00000254559 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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.837 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BET1L	NM_001098787.2 link	c.*1240A>G		3_prime_UTR_variant	Exon 4 of 4	ENST00000382762.8	NP_001092257.1	Q9NYM9
BET1L	NM_016526.5 link	c.*1408A>G		3_prime_UTR_variant	Exon 3 of 3		NP_057610.2	A0A0C4DH16

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
BET1L	ENST00000382762.8 link	c.*1240A>G	3_prime_UTR_variant	Exon 4 of 4	1	NM_001098787.2	ENSP00000372210.3	Q9NYM9
BET1L	ENST00000325147.13 link	c.*1408A>G	3_prime_UTR_variant	Exon 3 of 3	1		ENSP00000339093.7	A0A0C4DH16
ENSG00000254559	ENST00000526963.1 link	n.440T>C	non_coding_transcript_exon_variant	Exon 1 of 2	3
BET1L	ENST00000410108.5 link	c.168+1549A>G	intron_variant	Intron 3 of 5	3		ENSP00000386558.1	B8ZZS0

Frequencies

GnomAD3 genomes

AF:

0.689

AC:

104734

AN:

151994

Hom.:

37454

Cov.:

show subpopulations

Gnomad AFR

AF:

0.485

Gnomad AMI

AF:

0.849

Gnomad AMR

AF:

0.751

Gnomad ASJ

AF:

0.745

Gnomad EAS

AF:

0.858

Gnomad SAS

AF:

0.626

Gnomad FIN

AF:

0.796

Gnomad MID

AF:

0.794

Gnomad NFE

AF:

0.767

Gnomad OTH

AF:

0.736

GnomAD4 exome

AF:

0.764

AC:

469

AN:

614

Hom.:

177

Cov.:

AF XY:

0.780

AC XY:

326

AN XY:

418

show subpopulations

African (AFR)

AF:

0.600

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AF:

0.875

AC:

AN:

European-Finnish (FIN)

AF:

0.791

AC:

185

AN:

234

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.732

AC:

221

AN:

302

Other (OTH)

AF:

0.783

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

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:

0.689

AC:

104808

AN:

152112

Hom.:

37483

Cov.:

AF XY:

0.689

AC XY:

51270

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.485

AC:

20120

AN:

41454

American (AMR)

AF:

0.752

AC:

11502

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.745

AC:

2588

AN:

3472

East Asian (EAS)

AF:

0.858

AC:

4439

AN:

5176

South Asian (SAS)

AF:

0.626

AC:

3014

AN:

4818

European-Finnish (FIN)

AF:

0.796

AC:

8442

AN:

10600

Middle Eastern (MID)

AF:

0.789

AC:

232

AN:

294

European-Non Finnish (NFE)

AF:

0.767

AC:

52145

AN:

67976

Other (OTH)

AF:

0.737

AC:

1553

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1564

3128

4692

6256

7820

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

806

1612

2418

3224

4030

<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:

0.745

Hom.:

71685

Bravo

AF:

0.682

Asia WGS

AF:

0.722

AC:

2512

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.21

(source)

DANN

Benign

0.60

PhyloP100

-2.8

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over