rs11602954

Positions:

• chr11-202856-G-A

Variant summary

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

The ENST00000410108.5(BET1L):​c.168+2755C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 148,134 control chromosomes in the GnomAD database, including 2,511 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 0.16 (2502 hom., cov: 33)
  • Exomes 𝑓: 0.13 (9 hom.)
• Consequence: BET1L ENST00000410108.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.259

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]

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 (NFE) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BET1L	ENST00000410108.5	c.168+2755C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24131 AN: 147392 Hom.: 2501 Cov.: 33

Gnomad AFR AF: 0.0647

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.00283

Gnomad SAS AF: 0.0866

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.0762

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.160

GnomAD4 exome AF: 0.130 AC: 79 AN: 608 Hom.: 9 AF XY: 0.131 AC XY: 41 AN XY: 314

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.250

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.227

Gnomad4 NFE exome AF: 0.173

Gnomad4 OTH exome AF: 0.100

GnomAD4 genome AF: 0.164 AC: 24145 AN: 147526 Hom.: 2502 Cov.: 33 AF XY: 0.165 AC XY: 11918 AN XY: 72016

Gnomad4 AFR AF: 0.0646

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.00283

Gnomad4 SAS AF: 0.0868

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.158

Alfa AF: 0.191 Hom.: 5327

Bravo AF: 0.149

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.3
DANN	Benign	0.82

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11602954; hg19: chr11-202856;