rs6941094

Variant summary

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

The NM_002395.6(ME1):​c.78+2111G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 151,880 control chromosomes in the GnomAD database, including 9,811 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 0.35 ( 9811 hom., cov: 32)

Consequence

ME1
NM_002395.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.134
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=-0.94).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ME1NM_002395.6 linkuse as main transcriptc.78+2111G>T intron_variant ENST00000369705.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ME1ENST00000369705.4 linkuse as main transcriptc.78+2111G>T intron_variant 1 NM_002395.6 P1P48163-1

Frequencies

GnomAD3 genomes
AF:
0.352
AC:
53474
AN:
151762
Hom.:
9798
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.408
Gnomad AMI
AF:
0.486
Gnomad AMR
AF:
0.461
Gnomad ASJ
AF:
0.379
Gnomad EAS
AF:
0.266
Gnomad SAS
AF:
0.207
Gnomad FIN
AF:
0.285
Gnomad MID
AF:
0.484
Gnomad NFE
AF:
0.316
Gnomad OTH
AF:
0.391
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.352
AC:
53515
AN:
151880
Hom.:
9811
Cov.:
32
AF XY:
0.347
AC XY:
25740
AN XY:
74222
show subpopulations
Gnomad4 AFR
AF:
0.408
Gnomad4 AMR
AF:
0.462
Gnomad4 ASJ
AF:
0.379
Gnomad4 EAS
AF:
0.266
Gnomad4 SAS
AF:
0.206
Gnomad4 FIN
AF:
0.285
Gnomad4 NFE
AF:
0.316
Gnomad4 OTH
AF:
0.389
Alfa
AF:
0.334
Hom.:
12694
Bravo
AF:
0.377
Asia WGS
AF:
0.250
AC:
873
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
1.8
DANN
Benign
0.40

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: rs6941094; hg19: chr6-84138485; API