rs764051935

Variant names:

• chr16-721811-C-G
• rs764051935
• NM_023933.3:c.278C>G

Your query was ambiguous. Multiple possible variants found:

• chr16-721811-C-G
• chr16-721811-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_023933.3(ANTKMT):​c.278C>G​(p.Ala93Gly) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A93V) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 35)
• Consequence: ANTKMT NM_023933.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.87
• Publications: 0 publications found

Genes affected

ANTKMT (HGNC:14152): (adenine nucleotide translocase lysine methyltransferase) Enables protein-lysine N-methyltransferase activity. Involved in peptidyl-lysine trimethylation. Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_023933.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANTKMT	NM_023933.3	MANE Select	c.278C>G	p.Ala93Gly	missense	Exon 3 of 5	NP_076422.1	Q9BQD7
	ANTKMT	NM_001271285.2		c.278C>G	p.Ala93Gly	missense	Exon 3 of 4	NP_001258214.1	J3KMW5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANTKMT	ENST00000569529.6	TSL:1 MANE Select	c.278C>G	p.Ala93Gly	missense	Exon 3 of 5	ENSP00000454380.1	Q9BQD7
	ANTKMT	ENST00000853259.1		c.278C>G	p.Ala93Gly	missense	Exon 3 of 5	ENSP00000523318.1
	ANTKMT	ENST00000853260.1		c.278C>G	p.Ala93Gly	missense	Exon 3 of 5	ENSP00000523319.1

Frequencies

GnomAD3 genomes Cov.: 35

GnomAD4 exome Cov.: 62

GnomAD4 genome Cov.: 35

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.33
BayesDel_addAF	Uncertain	0.14	D
BayesDel_noAF	Uncertain	-0.040
CADD	Pathogenic	30
DANN	Uncertain	1.0
DEOGEN2	Benign	0.41	T
Eigen	Pathogenic	0.83
Eigen_PC	Pathogenic	0.75
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.92	D
M_CAP	Benign	0.033	D
MetaRNN	Uncertain	0.68	D
MetaSVM	Benign	-0.33	T
MutationAssessor	Pathogenic	3.6	H
PhyloP100		3.9
PrimateAI	Uncertain	0.65	T
PROVEAN	Uncertain	-3.9	D
REVEL	Uncertain	0.42
Sift	Uncertain	0.0060	D
Sift4G	Uncertain	0.028	D
Polyphen		1.0	D
Vest4		0.56
MutPred		0.54		Loss of stability (P = 0.0129)
MVP		0.55
MPC		0.45
ClinPred		1.0	D
GERP RS		5.1
PromoterAI		-0.020	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2
Varity_R		0.64
gMVP		0.80

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: rs764051935; hg19: chr16-771811;