11-13346203-T-C

Variant summary

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

The NM_001297719.2(BMAL1):c.-134-3742T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 152,136 control chromosomes in the GnomAD database, including 26,310 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 0.58 (26310 hom., cov: 33)
• Consequence: BMAL1 NM_001297719.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198

Genes affected

BMAL1 (HGNC:701): (basic helix-loop-helix ARNT like 1) The protein encoded by this gene is a basic helix-loop-helix protein that forms a heterodimer with CLOCK. This heterodimer binds E-box enhancer elements upstream of Period (PER1, PER2, PER3) and Cryptochrome (CRY1, CRY2) genes and activates transcription of these genes. PER and CRY proteins heterodimerize and repress their own transcription by interacting in a feedback loop with CLOCK/ARNTL complexes. Defects in this gene have been linked to infertility, problems with gluconeogenesis and lipogenesis, and altered sleep patterns. The protein regulates interferon-stimulated gene expression and is an important factor in viral infection, including COVID-19. [provided by RefSeq, Oct 2021]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BMAL1	NM_001297719.2	c.-134-3742T>C		intron_variant		ENST00000403290.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BMAL1	ENST00000403290.6	c.-134-3742T>C		intron_variant		1	NM_001297719.2	P4

Frequencies

GnomAD3 genomes AF: 0.580 AC: 88201 AN: 152018 Hom.: 26307 Cov.: 33

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.609

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.580 AC: 88236 AN: 152136 Hom.: 26310 Cov.: 33 AF XY: 0.569 AC XY: 42319 AN XY: 74366

Gnomad4 AFR AF: 0.527

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.330

Gnomad4 SAS AF: 0.524

Gnomad4 FIN AF: 0.519

Gnomad4 NFE AF: 0.661

Gnomad4 OTH AF: 0.610

Alfa AF: 0.623 Hom.: 19170

Bravo AF: 0.578

Asia WGS AF: 0.434 AC: 1512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	1.6
Dann	Benign	0.67

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: rs3816360; hg19: chr11-13367750;