5-10248063-A-T

Variant names:

• chr5-10248063-A-T
• rs2548552
• NM_199133.4:c.16+1795T>A

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+1795T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.736 in 152,192 control chromosomes in the GnomAD database, including 43,436 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 0.74 (43436 hom., cov: 33)
• Consequence: ATPSCKMT NM_199133.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.80
• Publications: 5 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=-1.02).
• 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+1795T>A		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+1795T>A		intron_variant	Intron 1 of 4	1	NM_199133.4	ENSP00000422338.1

Frequencies

GnomAD3 genomes AF: 0.736 AC: 111980 AN: 152076 Hom.: 43417 Cov.: 33

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.881

Gnomad EAS AF: 0.863

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.845

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.854

Gnomad OTH AF: 0.765

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

GnomAD4 genome AF: 0.736 AC: 112040 AN: 152192 Hom.: 43436 Cov.: 33 AF XY: 0.738 AC XY: 54947 AN XY: 74406

African (AFR) AF: 0.466 AC: 19351 AN: 41490

American (AMR) AF: 0.808 AC: 12362 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.881 AC: 3060 AN: 3472

East Asian (EAS) AF: 0.864 AC: 4472 AN: 5178

South Asian (SAS) AF: 0.648 AC: 3128 AN: 4824

European-Finnish (FIN) AF: 0.845 AC: 8957 AN: 10602

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.854 AC: 58086 AN: 68008

Other (OTH) AF: 0.767 AC: 1619 AN: 2112

Alfa AF: 0.728 Hom.: 2522

Bravo AF: 0.726

Asia WGS AF: 0.762 AC: 2648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.51
PhyloP100		-2.8
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: rs2548552; hg19: chr5-10248175;