Genetic Variant BET1L:c.*1514G>A (chr11-203788-C-T) – 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.*1514G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0488 in 153,284 control chromosomes in the GnomAD database, including 234 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 0.049 ( 234 hom., cov: 33)

Exomes 𝑓: 0.029 ( 0 hom. )

Consequence

BET1L
NM_001098787.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.38

Publications

48 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=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BET1L	NM_001098787.2 link	c.*1514G>A		3_prime_UTR_variant	Exon 4 of 4	ENST00000382762.8	NP_001092257.1
BET1L	NM_016526.5 link	c.*1682G>A		3_prime_UTR_variant	Exon 3 of 3		NP_057610.2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
BET1L	ENST00000382762.8 link	c.*1514G>A	3_prime_UTR_variant	Exon 4 of 4	1	NM_001098787.2	ENSP00000372210.3
BET1L	ENST00000325147.13 link	c.*1682G>A	3_prime_UTR_variant	Exon 3 of 3	1		ENSP00000339093.7
ENSG00000254559	ENST00000526963.1 link	n.166C>T	non_coding_transcript_exon_variant	Exon 1 of 2	3
BET1L	ENST00000410108.5 link	c.168+1823G>A	intron_variant	Intron 3 of 5	3		ENSP00000386558.1

Frequencies

GnomAD3 genomes

AF:

0.0490

AC:

7450

AN:

152184

Hom.:

235

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0598

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0455

Gnomad ASJ

AF:

0.0230

Gnomad EAS

AF:

0.145

Gnomad SAS

AF:

0.102

Gnomad FIN

AF:

0.0229

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0383

Gnomad OTH

AF:

0.0420

GnomAD4 exome

AF:

0.0285

AC:

AN:

982

Hom.:

Cov.:

AF XY:

0.0325

AC XY:

AN XY:

554

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.143

AC:

AN:

East Asian (EAS)

AF:

0.0536

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.0247

AC:

AN:

486

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0223

AC:

AN:

358

Other (OTH)

AF:

0.0556

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.0489

AC:

7445

AN:

152302

Hom.:

234

Cov.:

AF XY:

0.0493

AC XY:

3673

AN XY:

74470

show subpopulations

African (AFR)

AF:

0.0596

AC:

2479

AN:

41564

American (AMR)

AF:

0.0454

AC:

694

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.0230

AC:

AN:

3472

East Asian (EAS)

AF:

0.145

AC:

750

AN:

5174

South Asian (SAS)

AF:

0.102

AC:

493

AN:

4830

European-Finnish (FIN)

AF:

0.0229

AC:

243

AN:

10612

Middle Eastern (MID)

AF:

0.0442

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0383

AC:

2603

AN:

68030

Other (OTH)

AF:

0.0425

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

365

730

1094

1459

1824

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

184

276

368

460

<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:

0.0443

Hom.:

591

Bravo

AF:

0.0508

Asia WGS

AF:

0.119

AC:

413

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.25

(source)

DANN

Benign

0.52

PhyloP100

-2.4

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