NM_021117.5:c.*2015T>A

Variant names:

• chr11-45882926-T-A
• rs6798
• NM_021117.5:c.*2015T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_021117.5(CRY2):​c.*2015T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CRY2 NM_021117.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05
• Publications: 22 publications found

Genes affected

CRY2 (HGNC:2385): (cryptochrome circadian regulator 2) 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. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2014]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021117.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRY2	NM_021117.5	MANE Select	c.*2015T>A		3_prime_UTR	Exon 12 of 12	NP_066940.3
	CRY2	NM_001127457.3		c.*2015T>A		3_prime_UTR	Exon 12 of 12	NP_001120929.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRY2	ENST00000616080.2	TSL:1 MANE Select	c.*2015T>A		3_prime_UTR	Exon 12 of 12	ENSP00000484684.1
	CRY2	ENST00000443527.6	TSL:1	c.*2015T>A		3_prime_UTR	Exon 12 of 12	ENSP00000406751.2
	CRY2	ENST00000616623.4	TSL:1	c.*2015T>A		3_prime_UTR	Exon 12 of 12	ENSP00000478187.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 237594 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 120434

African (AFR) AF: 0.00 AC: 0 AN: 6994

American (AMR) AF: 0.00 AC: 0 AN: 7136

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 8984

East Asian (EAS) AF: 0.00 AC: 0 AN: 22332

South Asian (SAS) AF: 0.00 AC: 0 AN: 2096

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 19942

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1256

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 153064

Other (OTH) AF: 0.00 AC: 0 AN: 15790

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 26944

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.3
DANN	Benign	0.50
PhyloP100		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

Other links and lift over

dbSNP: rs6798; hg19: chr11-45904477;