5-10239881-A-G

Position:

• chr5-10239881-A-G

Variant summary

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

The NM_199133.4(ATPSCKMT):​c.17-525T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,186 control chromosomes in the GnomAD database, including 3,361 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 0.16 (3361 hom., cov: 32)
• Consequence: ATPSCKMT NM_199133.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.233

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ATPSCKMT	NM_199133.4	c.17-525T>C		intron_variant		ENST00000511437.6	NP_954584.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ATPSCKMT	ENST00000511437.6	c.17-525T>C		intron_variant		1	NM_199133.4	ENSP00000422338	P1

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23633 AN: 152068 Hom.: 3359 Cov.: 32

Gnomad AFR AF: 0.0681

Gnomad AMI AF: 0.0505

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.155 AC: 23648 AN: 152186 Hom.: 3361 Cov.: 32 AF XY: 0.168 AC XY: 12466 AN XY: 74394

Gnomad4 AFR AF: 0.0682

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.754

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.171

Alfa AF: 0.138 Hom.: 2430

Bravo AF: 0.164

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.4
DANN	Benign	0.54

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

Other links and lift over

dbSNP: rs2445871; hg19: chr5-10239993;