rs2280543

chr11-203788-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.38

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
BET1L	NM_001098787.2	c.*1514G>A		3_prime_UTR_variant	4/4	ENST00000382762.8
BET1L	NM_016526.5	c.*1682G>A		3_prime_UTR_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BET1L	ENST00000382762.8	c.*1514G>A		3_prime_UTR_variant	4/4	1	NM_001098787.2	P1
BET1L	ENST00000325147.13	c.*1682G>A		3_prime_UTR_variant	3/3	1
	ENST00000526963.1	n.166C>T		non_coding_transcript_exon_variant	1/2	3
BET1L	ENST00000410108.5	c.168+1823G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0490 AC: 7450 AN: 152184 Hom.: 235 Cov.: 33

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: 28 AN: 982 Hom.: 0 Cov.: 0 AF XY: 0.0325 AC XY: 18 AN XY: 554

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.143

Gnomad4 EAS exome AF: 0.0536

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0247

Gnomad4 NFE exome AF: 0.0223

Gnomad4 OTH exome AF: 0.0556

GnomAD4 genome AF: 0.0489 AC: 7445 AN: 152302 Hom.: 234 Cov.: 33 AF XY: 0.0493 AC XY: 3673 AN XY: 74470

Gnomad4 AFR AF: 0.0596

Gnomad4 AMR AF: 0.0454

Gnomad4 ASJ AF: 0.0230

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.0229

Gnomad4 NFE AF: 0.0383

Gnomad4 OTH AF: 0.0425

Alfa AF: 0.0420 Hom.: 211

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
Dann	Benign	0.52
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

LitVar

Other links and lift over

dbSNP: rs2280543; hg19: chr11-203788;