rs2847326

Positions:

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_017512.7(ENOSF1):​c.1149-826A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 152,128 control chromosomes in the GnomAD database, including 4,805 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 0.24 ( 4805 hom., cov: 32)

Consequence

ENOSF1
NM_017512.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.304
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ENOSF1NM_017512.7 linkuse as main transcriptc.1149-826A>T intron_variant ENST00000647584.2 NP_059982.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENOSF1ENST00000647584.2 linkuse as main transcriptc.1149-826A>T intron_variant NM_017512.7 ENSP00000497230 P1Q7L5Y1-1

Frequencies

GnomAD3 genomes
AF:
0.242
AC:
36822
AN:
152010
Hom.:
4797
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.285
Gnomad AMI
AF:
0.315
Gnomad AMR
AF:
0.277
Gnomad ASJ
AF:
0.131
Gnomad EAS
AF:
0.00346
Gnomad SAS
AF:
0.100
Gnomad FIN
AF:
0.251
Gnomad MID
AF:
0.123
Gnomad NFE
AF:
0.242
Gnomad OTH
AF:
0.217
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.242
AC:
36866
AN:
152128
Hom.:
4805
Cov.:
32
AF XY:
0.239
AC XY:
17742
AN XY:
74370
show subpopulations
Gnomad4 AFR
AF:
0.285
Gnomad4 AMR
AF:
0.277
Gnomad4 ASJ
AF:
0.131
Gnomad4 EAS
AF:
0.00347
Gnomad4 SAS
AF:
0.101
Gnomad4 FIN
AF:
0.251
Gnomad4 NFE
AF:
0.242
Gnomad4 OTH
AF:
0.215
Alfa
AF:
0.253
Hom.:
621
Bravo
AF:
0.247
Asia WGS
AF:
0.0620
AC:
219
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
10
DANN
Benign
0.82

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

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

Other links and lift over

dbSNP: rs2847326; hg19: chr18-676228; API