Variant chr7-141614171-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_018238.4(AGK):c.416C>A(p.Thr139Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000195 in 1,537,864 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0000014 ( 1 hom. )

Consequence

AGK
NM_018238.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.40

Variant links:

Genes affected

AGK (HGNC:21869): (acylglycerol kinase) The protein encoded by this gene is a mitochondrial membrane protein involved in lipid and glycerolipid metabolism. The encoded protein is a lipid kinase that catalyzes the formation of phosphatidic and lysophosphatidic acids. Defects in this gene have been associated with mitochondrial DNA depletion syndrome 10. [provided by RefSeq, Feb 2012]

AGK links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.07265186).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
AGK	NM_018238.4 linkuse as main transcript	c.416C>A	p.Thr139Lys	missense_variant	7/16	ENST00000649286.2	NP_060708.1
AGK	NM_001364948.3 linkuse as main transcript	c.416C>A	p.Thr139Lys	missense_variant	7/15		NP_001351877.1
AGK	XM_011516397.4 linkuse as main transcript	c.416C>A	p.Thr139Lys	missense_variant	7/16		XP_011514699.1
AGK	XM_024446835.2 linkuse as main transcript	c.416C>A	p.Thr139Lys	missense_variant	7/16		XP_024302603.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AGK	ENST00000649286.2 linkuse as main transcript	c.416C>A	p.Thr139Lys	missense_variant	7/16		NM_018238.4	ENSP00000497280	P1	Q53H12-1

Frequencies

GnomAD3 genomes

AF:

0.00000657

AC:

AN:

152128

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.00000144

AC:

AN:

1385618

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

690996

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000257

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.00000657

AC:

AN:

152246

Hom.:

Cov.:

AF XY:

0.0000134

AC XY:

AN XY:

74442

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.094

BayesDel_addAF

Benign

-0.26

BayesDel_noAF

Benign

-0.61

CADD

Benign

DANN

Benign

0.76

DEOGEN2

Benign

0.037

T;T;T;.;T;.;.;T;T;.

Eigen

Benign

-0.49

Eigen_PC

Benign

-0.29

FATHMM_MKL

Uncertain

0.81

LIST_S2

Uncertain

0.93

.;D;D;D;.;D;D;.;D;D

M_CAP

Benign

0.0043

MetaRNN

Benign

0.073

T;T;T;T;T;T;T;T;T;T

MetaSVM

Benign

-0.98

MutationAssessor

Benign

-0.34

N;.;.;.;N;.;.;N;N;.

MutationTaster

Benign

0.98

N;N;N

PrimateAI

Benign

0.38

PROVEAN

Benign

0.43

N;.;N;.;.;.;.;.;.;.

REVEL

Benign

0.034

Sift

Benign

0.84

T;.;T;.;.;.;.;.;.;.

Sift4G

Benign

0.89

T;T;T;.;.;.;.;.;.;.

Polyphen

0.0

B;.;.;.;B;.;.;B;B;.

Vest4

0.27

MutPred

0.56

Gain of ubiquitination at T139 (P = 0.0238);.;.;.;Gain of ubiquitination at T139 (P = 0.0238);.;.;Gain of ubiquitination at T139 (P = 0.0238);Gain of ubiquitination at T139 (P = 0.0238);Gain of ubiquitination at T139 (P = 0.0238);

MVP

0.12

MPC

0.25

ClinPred

0.21

GERP RS

1.6

Varity_R

0.12

gMVP

0.32

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

No publications associated with this variant yet.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over