chr5-10246898-T-C

Variant names:

• chr5-10246898-T-C
• rs2548554
• NM_199133.4:c.16+2960A>G

Variant summary

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

The NM_199133.4(ATPSCKMT):​c.16+2960A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.751 in 152,102 control chromosomes in the GnomAD database, including 44,582 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 0.75 (44582 hom., cov: 32)
• Consequence: ATPSCKMT NM_199133.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200
• Publications: 8 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATPSCKMT	NM_199133.4	c.16+2960A>G		intron_variant	Intron 1 of 4	ENST00000511437.6	NP_954584.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATPSCKMT	ENST00000511437.6	c.16+2960A>G		intron_variant	Intron 1 of 4	1	NM_199133.4	ENSP00000422338.1

Frequencies

GnomAD3 genomes AF: 0.751 AC: 114196 AN: 151984 Hom.: 44562 Cov.: 32

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.815

Gnomad ASJ AF: 0.879

Gnomad EAS AF: 0.864

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.854

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.751 AC: 114259 AN: 152102 Hom.: 44582 Cov.: 32 AF XY: 0.753 AC XY: 55980 AN XY: 74368

African (AFR) AF: 0.518 AC: 21451 AN: 41442

American (AMR) AF: 0.815 AC: 12459 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.879 AC: 3051 AN: 3472

East Asian (EAS) AF: 0.864 AC: 4465 AN: 5168

South Asian (SAS) AF: 0.649 AC: 3125 AN: 4814

European-Finnish (FIN) AF: 0.846 AC: 8953 AN: 10584

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.854 AC: 58105 AN: 68016

Other (OTH) AF: 0.779 AC: 1643 AN: 2108

Alfa AF: 0.773 Hom.: 5054

Bravo AF: 0.743

Asia WGS AF: 0.764 AC: 2655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.8
DANN	Benign	0.70
PhyloP100		0.0020
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: rs2548554; hg19: chr5-10247010;