rs774027

Variant names:

• chr12-56428594-T-A
• rs774027
• NM_003920.5:c.1363A>T

Your query was ambiguous. Multiple possible variants found:

• chr12-56428594-T-A
• chr12-56428594-T-C
• chr12-56428594-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003920.5(TIMELESS):​c.1363A>T​(p.Ile455Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 1,613,532 control chromosomes in the GnomAD database, including 172,069 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.42 (14833 hom., cov: 31)
  • Exomes 𝑓: 0.46 (157236 hom.)
• Consequence: TIMELESS NM_003920.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.566
• Publications: 45 publications found

Genes affected

TIMELESS (HGNC:11813): (timeless circadian regulator) The protein encoded by this gene is highly conserved and is involved in cell survival after damage or stress, increase in DNA polymerase epsilon activity, maintenance of telomere length, and epithelial cell morphogenesis. The encoded protein also plays a role in the circadian rhythm autoregulatory loop, interacting with the PERIOD genes (PER1, PER2, and PER3) and others to downregulate activation of PER1 by CLOCK/ARNTL. Changes in this gene or its expression may promote prostate cancer, lung cancer, breast cancer, and mental disorders. [provided by RefSeq, Feb 2014]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=8.541583E-7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003920.5. 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
	TIMELESS	NM_003920.5	MANE Select	c.1363A>T	p.Ile455Leu	missense	Exon 12 of 29	NP_003911.2
	TIMELESS	NM_001330295.2		c.1360A>T	p.Ile454Leu	missense	Exon 12 of 29	NP_001317224.1
	TIMELESS	NR_138471.2		n.1541A>T		non_coding_transcript_exon	Exon 12 of 29

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TIMELESS	ENST00000553532.6	TSL:1 MANE Select	c.1363A>T	p.Ile455Leu	missense	Exon 12 of 29	ENSP00000450607.1
	TIMELESS	ENST00000229201.4	TSL:5	c.1360A>T	p.Ile454Leu	missense	Exon 12 of 29	ENSP00000229201.4

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64203 AN: 151874 Hom.: 14825 Cov.: 31

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.498

GnomAD2 exomes AF: 0.505 AC: 126268 AN: 249882 AF XY: 0.500

Gnomad AFR exome AF: 0.259

Gnomad AMR exome AF: 0.714

Gnomad ASJ exome AF: 0.523

Gnomad EAS exome AF: 0.748

Gnomad FIN exome AF: 0.416

Gnomad NFE exome AF: 0.454

Gnomad OTH exome AF: 0.505

GnomAD4 exome AF: 0.457 AC: 668422 AN: 1461540 Hom.: 157236 Cov.: 48 AF XY: 0.458 AC XY: 333156 AN XY: 727078

African (AFR) AF: 0.255 AC: 8535 AN: 33466

American (AMR) AF: 0.701 AC: 31326 AN: 44716

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 13770 AN: 26134

East Asian (EAS) AF: 0.673 AC: 26712 AN: 39698

South Asian (SAS) AF: 0.499 AC: 43017 AN: 86246

European-Finnish (FIN) AF: 0.423 AC: 22587 AN: 53382

Middle Eastern (MID) AF: 0.572 AC: 3292 AN: 5760

European-Non Finnish (NFE) AF: 0.441 AC: 490562 AN: 1111748

Other (OTH) AF: 0.474 AC: 28621 AN: 60390

GnomAD4 genome AF: 0.423 AC: 64231 AN: 151992 Hom.: 14833 Cov.: 31 AF XY: 0.426 AC XY: 31647 AN XY: 74296

African (AFR) AF: 0.267 AC: 11058 AN: 41486

American (AMR) AF: 0.581 AC: 8857 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1840 AN: 3464

East Asian (EAS) AF: 0.733 AC: 3781 AN: 5156

South Asian (SAS) AF: 0.503 AC: 2419 AN: 4810

European-Finnish (FIN) AF: 0.407 AC: 4293 AN: 10550

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.448 AC: 30432 AN: 67960

Other (OTH) AF: 0.494 AC: 1042 AN: 2110

Alfa AF: 0.453 Hom.: 5476

Bravo AF: 0.438

TwinsUK AF: 0.418 AC: 1549

ALSPAC AF: 0.441 AC: 1701

ESP6500AA AF: 0.270 AC: 1188

ESP6500EA AF: 0.454 AC: 3907

ExAC AF: 0.493 AC: 59829

Asia WGS AF: 0.570 AC: 1985 AN: 3478

EpiCase AF: 0.458

EpiControl AF: 0.467

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.058
BayesDel_addAF	Benign	-0.77	T
BayesDel_noAF	Benign	-0.73
CADD	Benign	2.5
DANN	Benign	0.42
DEOGEN2	Benign	0.043	T
Eigen	Benign	-1.6
Eigen_PC	Benign	-1.6
FATHMM_MKL	Benign	0.14	N
LIST_S2	Benign	0.32	T
MetaRNN	Benign	8.5e-7	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.0	N
PhyloP100		0.57
PrimateAI	Benign	0.25	T
PROVEAN	Benign	0.73	N
REVEL	Benign	0.016
Sift	Benign	0.53	T
Sift4G	Benign	0.57	T
Polyphen		0.0	B
Vest4		0.077
MutPred		0.33		Gain of catalytic residue at M453 (P = 0.0075)
MPC		0.11
ClinPred		0.000015	T
GERP RS		-2.3
Varity_R		0.033
gMVP		0.15
Mutation Taster		=99/1	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs774027; hg19: chr12-56822378; COSMIC: COSV57511395; COSMIC: COSV57511395;