5-10225913-T-C

Position:

• chr5-10225913-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_199133.4(ATPSCKMT):​c.*1528A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 152,020 control chromosomes in the GnomAD database, including 29,373 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 0.61 (29373 hom., cov: 31)
• Consequence: ATPSCKMT NM_199133.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATPSCKMT	NM_199133.4	c.*1528A>G		3_prime_UTR_variant	5/5	ENST00000511437.6	NP_954584.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATPSCKMT	ENST00000511437.6	c.*1528A>G		3_prime_UTR_variant	5/5	1	NM_199133.4	ENSP00000422338	P1

Frequencies

GnomAD3 genomes AF: 0.607 AC: 92274 AN: 151902 Hom.: 29346 Cov.: 31

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.607 AC: 92336 AN: 152020 Hom.: 29373 Cov.: 31 AF XY: 0.617 AC XY: 45834 AN XY: 74326

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.723

Gnomad4 ASJ AF: 0.730

Gnomad4 EAS AF: 0.834

Gnomad4 SAS AF: 0.732

Gnomad4 FIN AF: 0.678

Gnomad4 NFE AF: 0.655

Gnomad4 OTH AF: 0.618

Alfa AF: 0.650 Hom.: 14433

Bravo AF: 0.602

Asia WGS AF: 0.725 AC: 2520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.0
DANN	Benign	0.74

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1355096; hg19: chr5-10226025;