rs1180242

Variant summary

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

The NM_002395.6(ME1):​c.1548+662A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 152,142 control chromosomes in the GnomAD database, including 31,762 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 0.62 ( 31762 hom., cov: 33)

Consequence

ME1
NM_002395.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.66
Variant links:
Genes affected
ME1 (HGNC:6983): (malic enzyme 1) This gene encodes a cytosolic, NADP-dependent enzyme that generates NADPH for fatty acid biosynthesis. The activity of this enzyme, the reversible oxidative decarboxylation of malate, links the glycolytic and citric acid cycles. The regulation of expression for this gene is complex. Increased expression can result from elevated levels of thyroid hormones or by higher proportions of carbohydrates in the diet. [provided by RefSeq, Jul 2008]

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=-0.79).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ME1NM_002395.6 linkuse as main transcriptc.1548+662A>G intron_variant ENST00000369705.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ME1ENST00000369705.4 linkuse as main transcriptc.1548+662A>G intron_variant 1 NM_002395.6 P1P48163-1

Frequencies

GnomAD3 genomes
AF:
0.620
AC:
94229
AN:
152024
Hom.:
31699
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.906
Gnomad AMI
AF:
0.465
Gnomad AMR
AF:
0.597
Gnomad ASJ
AF:
0.553
Gnomad EAS
AF:
0.454
Gnomad SAS
AF:
0.431
Gnomad FIN
AF:
0.460
Gnomad MID
AF:
0.636
Gnomad NFE
AF:
0.507
Gnomad OTH
AF:
0.613
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.620
AC:
94347
AN:
152142
Hom.:
31762
Cov.:
33
AF XY:
0.611
AC XY:
45431
AN XY:
74370
show subpopulations
Gnomad4 AFR
AF:
0.907
Gnomad4 AMR
AF:
0.597
Gnomad4 ASJ
AF:
0.553
Gnomad4 EAS
AF:
0.455
Gnomad4 SAS
AF:
0.430
Gnomad4 FIN
AF:
0.460
Gnomad4 NFE
AF:
0.507
Gnomad4 OTH
AF:
0.613
Alfa
AF:
0.534
Hom.:
29413
Bravo
AF:
0.647
Asia WGS
AF:
0.480
AC:
1672
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
2.0
DANN
Benign
0.42

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: rs1180242; hg19: chr6-83925555; API