dbSNP rs2280544: 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

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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