dbSNP rs1059384: ENOSF1:n.*1029A>G (chr18-673995-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000581475.5(ENOSF1):n.*1029A>G variant causes a non coding transcript exon 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
ENST00000581475.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.128

Publications

13 publications found

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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
ENOSF1	NM_017512.7 link	c.*310A>G		3_prime_UTR_variant	Exon 16 of 16	ENST00000647584.2	NP_059982.2	Q7L5Y1-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENOSF1	ENST00000647584.2 link	c.*310A>G		3_prime_UTR_variant	Exon 16 of 16		NM_017512.7	ENSP00000497230.2		Q7L5Y1-1

Frequencies

GnomAD3 genomes

AF:

0.397

AC:

60312

AN:

151736

Hom.:

13083

Cov.:

show subpopulations

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.:

AF XY:

0.357

AC XY:

10115

AN XY:

28314

show subpopulations

African (AFR)

AF:

0.567

AC:

986

AN:

1738

American (AMR)

AF:

0.326

AC:

648

AN:

1986

Ashkenazi Jewish (ASJ)

AF:

0.394

AC:

778

AN:

1976

East Asian (EAS)

AF:

0.702

AC:

2110

AN:

3004

South Asian (SAS)

AF:

0.425

AC:

1434

AN:

3378

European-Finnish (FIN)

AF:

0.309

AC:

822

AN:

2664

Middle Eastern (MID)

AF:

0.448

AC:

120

AN:

268

European-Non Finnish (NFE)

AF:

0.309

AC:

11336

AN:

36682

Other (OTH)

AF:

0.368

AC:

1387

AN:

3774

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

635

1270

1905

2540

3175

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

156

234

312

390

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.397

AC:

60359

AN:

151854

Hom.:

13098

Cov.:

AF XY:

0.401

AC XY:

29789

AN XY:

74214

show subpopulations

African (AFR)

AF:

0.552

AC:

22830

AN:

41368

American (AMR)

AF:

0.335

AC:

5111

AN:

15244

Ashkenazi Jewish (ASJ)

AF:

0.398

AC:

1381

AN:

3466

East Asian (EAS)

AF:

0.685

AC:

3538

AN:

5166

South Asian (SAS)

AF:

0.446

AC:

2146

AN:

4808

European-Finnish (FIN)

AF:

0.303

AC:

3195

AN:

10540

Middle Eastern (MID)

AF:

0.473

AC:

139

AN:

294

European-Non Finnish (NFE)

AF:

0.309

AC:

21024

AN:

67948

Other (OTH)

AF:

0.400

AC:

843

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1750

3500

5251

7001

8751

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

566

1132

1698

2264

2830

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.328

Hom.:

9542

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

(source)

DANN

Benign

0.47

PhyloP100

0.13

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over