dbSNP rs2280543: 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

49 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001098787.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BET1L	NM_001098787.2	MANE Select	c.*1514G>A		3_prime_UTR	Exon 4 of 4	NP_001092257.1	Q9NYM9
	BET1L	NM_016526.5		c.*1682G>A		3_prime_UTR	Exon 3 of 3	NP_057610.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
BET1L	ENST00000382762.8	TSL:1 MANE Select	c.*1514G>A	3_prime_UTR	Exon 4 of 4	ENSP00000372210.3	Q9NYM9
BET1L	ENST00000325147.13	TSL:1	c.*1682G>A	3_prime_UTR	Exon 3 of 3	ENSP00000339093.7	A0A0C4DH16
BET1L	ENST00000410108.5	TSL:3	c.168+1823G>A	intron	N/A	ENSP00000386558.1	B8ZZS0

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 v4.9

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

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