rs1144184

Variant names:

• chr6-83308202-T-C
• rs1144184
• NM_002395.6:c.704+7108A>G

Your query was ambiguous. Multiple possible variants found:

• chr6-83308202-T-C
• chr6-83308202-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002395.6(ME1):​c.704+7108A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 151,914 control chromosomes in the GnomAD database, including 19,230 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 0.48 (19230 hom., cov: 32)
• Consequence: ME1 NM_002395.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149
• Publications: 6 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002395.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ME1	NM_002395.6	MANE Select	c.704+7108A>G		intron	N/A	NP_002386.1	P48163-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ME1	ENST00000369705.4	TSL:1 MANE Select	c.704+7108A>G		intron	N/A	ENSP00000358719.3	P48163-1
	ME1	ENST00000956348.1		c.818+7108A>G		intron	N/A	ENSP00000626407.1
	ME1	ENST00000956344.1		c.758+7108A>G		intron	N/A	ENSP00000626403.1

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72891 AN: 151796 Hom.: 19188 Cov.: 32

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.494

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.480 AC: 72989 AN: 151914 Hom.: 19230 Cov.: 32 AF XY: 0.477 AC XY: 35366 AN XY: 74216

African (AFR) AF: 0.700 AC: 29025 AN: 41450

American (AMR) AF: 0.533 AC: 8118 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1459 AN: 3470

East Asian (EAS) AF: 0.410 AC: 2113 AN: 5158

South Asian (SAS) AF: 0.302 AC: 1456 AN: 4822

European-Finnish (FIN) AF: 0.383 AC: 4035 AN: 10538

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.370 AC: 25162 AN: 67924

Other (OTH) AF: 0.492 AC: 1038 AN: 2110

Alfa AF: 0.409 Hom.: 55918

Bravo AF: 0.508

Asia WGS AF: 0.383 AC: 1333 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.34
PhyloP100		-0.15
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1144184; hg19: chr6-84017921;