rs1059384

Positions:

• chr18-673995-T-C
• chr18-673995-T-G

Variant summary

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

The NM_017512.7(ENOSF1):​c.*310A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 207,324 control chromosomes in the GnomAD database, including 16,879 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 0.40 (13098 hom., cov: 31)
  • Exomes 𝑓: 0.35 (3781 hom.)
• Consequence: ENOSF1 NM_017512.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.128

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ENOSF1	NM_017512.7	c.*310A>G		3_prime_UTR_variant	16/16	ENST00000647584.2	NP_059982.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENOSF1	ENST00000647584	c.*310A>G		3_prime_UTR_variant	16/16		NM_017512.7	ENSP00000497230.2

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60312 AN: 151736 Hom.: 13083 Cov.: 31

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.397

GnomAD4 exome AF: 0.354 AC: 19621 AN: 55470 Hom.: 3781 Cov.: 0 AF XY: 0.357 AC XY: 10115 AN XY: 28314

Gnomad4 AFR exome AF: 0.567

Gnomad4 AMR exome AF: 0.326

Gnomad4 ASJ exome AF: 0.394

Gnomad4 EAS exome AF: 0.702

Gnomad4 SAS exome AF: 0.425

Gnomad4 FIN exome AF: 0.309

Gnomad4 NFE exome AF: 0.309

Gnomad4 OTH exome AF: 0.368

GnomAD4 genome AF: 0.397 AC: 60359 AN: 151854 Hom.: 13098 Cov.: 31 AF XY: 0.401 AC XY: 29789 AN XY: 74214

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.685

Gnomad4 SAS AF: 0.446

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.400

Alfa AF: 0.324 Hom.: 7817

Bravo AF: 0.407

Asia WGS AF: 0.575 AC: 2003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.47

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: rs1059384; hg19: chr18-673995;