12-107048537-C-T

Variant summary

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

The NM_004075.5(CRY1):c.159-26345G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,084 control chromosomes in the GnomAD database, including 1,961 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 0.12 (1961 hom., cov: 32)
• Consequence: CRY1 NM_004075.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.501

Genes affected

CRY1 (HGNC:2384): (cryptochrome circadian regulator 1) This gene encodes a flavin adenine dinucleotide-binding protein that is a key component of the circadian core oscillator complex, which regulates the circadian clock. This gene is upregulated by CLOCK/ARNTL heterodimers but then represses this upregulation in a feedback loop using PER/CRY heterodimers to interact with CLOCK/ARNTL. Polymorphisms in this gene have been associated with altered sleep patterns. The encoded protein is widely conserved across plants and animals. Loss of the related gene in mouse results in a shortened circadian cycle in complete darkness. [provided by RefSeq, Jan 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CRY1	NM_004075.5	c.159-26345G>A		intron_variant		ENST00000008527.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CRY1	ENST00000008527.10	c.159-26345G>A		intron_variant		1	NM_004075.5	P1
CRY1	ENST00000552790.5	n.488+1234G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18790 AN: 151966 Hom.: 1959 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.0732

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.0633

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0371

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.124 AC: 18817 AN: 152084 Hom.: 1961 Cov.: 32 AF XY: 0.126 AC XY: 9355 AN XY: 74356

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.0732

Gnomad4 EAS AF: 0.228

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.0633

Gnomad4 NFE AF: 0.0371

Gnomad4 OTH AF: 0.113

Alfa AF: 0.0818 Hom.: 120

Bravo AF: 0.134

Asia WGS AF: 0.199 AC: 690 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	4.4
Dann	Benign	0.84

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: rs11613557; hg19: chr12-107442315;