Variant rs11280056 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_017512.7(ENOSF1):c.*856_*861delCTTTAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 217,316 control chromosomes in the GnomAD database, including 17,511 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.39 ( 12782 hom., cov: 0)

Exomes 𝑓: 0.36 ( 4729 hom. )

Consequence

ENOSF1
NM_017512.7 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.42

Variant links:

Genes affected

ENOSF1 (HGNC:30365): (enolase superfamily member 1) This gene can encode a mitochondrial enzyme that is thought to convert L-fuconate to 2-keto-3-deoxy-L-fuconate. This locus was originally identified as the source of antisense RNAs of the adjacent thymidylate synthase gene. Splice variants at this locus may contain an alternate 3' exon that is complementary to the 3'UTR and terminal intron of the thymidylate synthase (TS) RNA and may downregulate TS expression. [provided by RefSeq, Aug 2017]

ENOSF1 links:

TYMS (HGNC:12441): (thymidylate synthetase) Thymidylate synthase catalyzes the methylation of deoxyuridylate to deoxythymidylate using, 10-methylenetetrahydrofolate (methylene-THF) as a cofactor. This function maintains the dTMP (thymidine-5-prime monophosphate) pool critical for DNA replication and repair. The enzyme has been of interest as a target for cancer chemotherapeutic agents. It is considered to be the primary site of action for 5-fluorouracil, 5-fluoro-2-prime-deoxyuridine, and some folate analogs. Expression of this gene and that of a naturally occurring antisense transcript, mitochondrial enolase superfamily member 1 (GeneID:55556), vary inversely when cell-growth progresses from late-log to plateau phase. Polymorphisms in this gene may be associated with etiology of neoplasia, including breast cancer, and response to chemotherapy. [provided by RefSeq, Aug 2017]

TYMS links:

ENOSF1 (HGNC:):

ENOSF1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ENOSF1	NM_017512.7 linkuse as main transcript	c.856_861delCTTTAA		3_prime_UTR_variant	16/16	ENST00000647584.2	NP_059982.2	Q7L5Y1-1
TYMS	NM_001071.4 linkuse as main transcript	c.450_455delAAGTTA		3_prime_UTR_variant	7/7	ENST00000323274.15	NP_001062.1	P04818-1Q53Y97

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENOSF1	ENST00000647584 linkuse as main transcript	c.856_861delCTTTAA		3_prime_UTR_variant	16/16		NM_017512.7	ENSP00000497230.2		Q7L5Y1-1
TYMS	ENST00000323274.15 linkuse as main transcript	c.450_455delAAGTTA		3_prime_UTR_variant	7/7	1	NM_001071.4	ENSP00000315644.10		P04818-1

Frequencies

GnomAD3 genomes

AF:

0.395

AC:

59744

AN:

151380

Hom.:

12769

Cov.:

show subpopulations

Gnomad AFR

AF:

0.547

Gnomad AMI

AF:

0.165

Gnomad AMR

AF:

0.333

Gnomad ASJ

AF:

0.398

Gnomad EAS

AF:

0.680

Gnomad SAS

AF:

0.448

Gnomad FIN

AF:

0.301

Gnomad MID

AF:

0.471

Gnomad NFE

AF:

0.308

Gnomad OTH

AF:

0.396

GnomAD4 exome

AF:

0.358

AC:

23543

AN:

65816

Hom.:

4729

AF XY:

0.354

AC XY:

10768

AN XY:

30388

show subpopulations

Gnomad4 AFR exome

AF:

0.525

Gnomad4 AMR exome

AF:

0.289

Gnomad4 ASJ exome

AF:

0.361

Gnomad4 EAS exome

AF:

0.633

Gnomad4 SAS exome

AF:

0.416

Gnomad4 FIN exome

AF:

0.250

Gnomad4 NFE exome

AF:

0.290

Gnomad4 OTH exome

AF:

0.336

GnomAD4 genome

AF:

0.395

AC:

59790

AN:

151500

Hom.:

12782

Cov.:

AF XY:

0.398

AC XY:

29482

AN XY:

74028

show subpopulations

Gnomad4 AFR

AF:

0.547

Gnomad4 AMR

AF:

0.333

Gnomad4 ASJ

AF:

0.398

Gnomad4 EAS

AF:

0.680

Gnomad4 SAS

AF:

0.445

Gnomad4 FIN

AF:

0.301

Gnomad4 NFE

AF:

0.308

Gnomad4 OTH

AF:

0.398

Alfa

AF:

0.346

Hom.:

1165

Bravo

AF:

0.406

Asia WGS

AF:

0.574

AC:

1997

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over