rs2280544

Positions:

• chr11-204062-T-C

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.80

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=-0.91).
• 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/exons	MANE	UniProt
BET1L	NM_001098787.2	c.*1240A>G		3_prime_UTR_variant	4/4	ENST00000382762.8
BET1L	NM_016526.5	c.*1408A>G		3_prime_UTR_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BET1L	ENST00000382762.8	c.*1240A>G		3_prime_UTR_variant	4/4	1	NM_001098787.2	P1
BET1L	ENST00000325147.13	c.*1408A>G		3_prime_UTR_variant	3/3	1
	ENST00000526963.1	n.440T>C		non_coding_transcript_exon_variant	1/2	3
BET1L	ENST00000410108.5	c.168+1549A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104734 AN: 151994 Hom.: 37454 Cov.: 33

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.: 0 AF XY: 0.780 AC XY: 326 AN XY: 418

Gnomad4 AFR exome AF: 0.600

Gnomad4 AMR exome AF: 1.00

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.875

Gnomad4 FIN exome AF: 0.791

Gnomad4 NFE exome AF: 0.732

Gnomad4 OTH exome AF: 0.783

GnomAD4 genome AF: 0.689 AC: 104808 AN: 152112 Hom.: 37483 Cov.: 33 AF XY: 0.689 AC XY: 51270 AN XY: 74364

Gnomad4 AFR AF: 0.485

Gnomad4 AMR AF: 0.752

Gnomad4 ASJ AF: 0.745

Gnomad4 EAS AF: 0.858

Gnomad4 SAS AF: 0.626

Gnomad4 FIN AF: 0.796

Gnomad4 NFE AF: 0.767

Gnomad4 OTH AF: 0.737

Alfa AF: 0.752 Hom.: 57666

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
DANN	Benign	0.60
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: rs2280544; hg19: chr11-204062;