Variant 5-10239149-G-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_199133.4(ATPSCKMT):c.224C>T(p.Thr75Met) variant causes a missense change. The variant allele was found at a frequency of 0.179 in 1,613,942 control chromosomes in the GnomAD database, including 39,939 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. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.19 ( 4105 hom., cov: 33)

Exomes 𝑓: 0.18 ( 35834 hom. )

Consequence

ATPSCKMT
NM_199133.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.12

Variant links:

Genes affected

ATPSCKMT (HGNC:27029): (ATP synthase c subunit lysine N-methyltransferase) Enables protein-lysine N-methyltransferase activity. Involved in peptidyl-lysine trimethylation; positive regulation of sensory perception of pain; and regulation of proton transport. Located in mitochondrial crista. [provided by Alliance of Genome Resources, Apr 2022]

ATPSCKMT links:

ATPSCKMT (HGNC:):

ATPSCKMT links:

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 (MetaRNN=2.826355E-6).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATPSCKMT	NM_199133.4 linkuse as main transcript	c.224C>T	p.Thr75Met	missense_variant	2/5	ENST00000511437.6	NP_954584.2	Q6P4H8-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATPSCKMT	ENST00000511437.6 linkuse as main transcript	c.224C>T	p.Thr75Met	missense_variant	2/5	1	NM_199133.4	ENSP00000422338.1		Q6P4H8-1

Frequencies

GnomAD3 genomes

AF:

0.190

AC:

28853

AN:

151982

Hom.:

4097

Cov.:

show subpopulations

Gnomad AFR

AF:

0.139

Gnomad AMI

AF:

0.102

Gnomad AMR

AF:

0.326

Gnomad ASJ

AF:

0.208

Gnomad EAS

AF:

0.772

Gnomad SAS

AF:

0.317

Gnomad FIN

AF:

0.175

Gnomad MID

AF:

0.237

Gnomad NFE

AF:

0.139

Gnomad OTH

AF:

0.201

GnomAD3 exomes

AF:

0.259

AC:

64684

AN:

249522

Hom.:

12904

AF XY:

0.250

AC XY:

33849

AN XY:

135380

show subpopulations

Gnomad AFR exome

AF:

0.136

Gnomad AMR exome

AF:

0.465

Gnomad ASJ exome

AF:

0.206

Gnomad EAS exome

AF:

0.770

Gnomad SAS exome

AF:

0.309

Gnomad FIN exome

AF:

0.183

Gnomad NFE exome

AF:

0.140

Gnomad OTH exome

AF:

0.229

GnomAD4 exome

AF:

0.178

AC:

260668

AN:

1461842

Hom.:

35834

Cov.:

AF XY:

0.181

AC XY:

131676

AN XY:

727214

show subpopulations

Gnomad4 AFR exome

AF:

0.140

Gnomad4 AMR exome

AF:

0.444

Gnomad4 ASJ exome

AF:

0.213

Gnomad4 EAS exome

AF:

0.819

Gnomad4 SAS exome

AF:

0.305

Gnomad4 FIN exome

AF:

0.179

Gnomad4 NFE exome

AF:

0.134

Gnomad4 OTH exome

AF:

0.202

GnomAD4 genome

AF:

0.190

AC:

28884

AN:

152100

Hom.:

4105

Cov.:

AF XY:

0.202

AC XY:

14987

AN XY:

74350

show subpopulations

Gnomad4 AFR

AF:

0.139

Gnomad4 AMR

AF:

0.326

Gnomad4 ASJ

AF:

0.208

Gnomad4 EAS

AF:

0.773

Gnomad4 SAS

AF:

0.317

Gnomad4 FIN

AF:

0.175

Gnomad4 NFE

AF:

0.139

Gnomad4 OTH

AF:

0.202

Alfa

AF:

0.168

Hom.:

7916

Bravo

AF:

0.201

TwinsUK

AF:

0.122

AC:

451

ALSPAC

AF:

0.128

AC:

494

ESP6500AA

AF:

0.127

AC:

519

ESP6500EA

AF:

0.138

AC:

1149

ExAC

AF:

0.246

AC:

29752

Asia WGS

AF:

0.519

AC:

1800

AN:

3478

EpiCase

AF:

0.141

EpiControl

AF:

0.140

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.61

BayesDel_noAF

Benign

-0.51

CADD

Uncertain

DANN

Uncertain

0.99

DEOGEN2

Benign

0.054

T;.

Eigen

Uncertain

0.21

Eigen_PC

Benign

0.20

FATHMM_MKL

Uncertain

0.91

LIST_S2

Uncertain

0.95

D;D

MetaRNN

Benign

0.0000028

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.6

M;M

PrimateAI

Benign

0.39

PROVEAN

Uncertain

-2.7

D;D

REVEL

Benign

0.14

Sift

Benign

0.063

T;D

Sift4G

Benign

0.082

T;T

Polyphen

0.076

B;.

Vest4

0.080

MPC

0.28

ClinPred

0.025

GERP RS

5.2

Varity_R

0.073

gMVP

0.52

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over