rs760194287

Variant names:

• chr16-722465-G-A
• rs760194287
• NM_023933.3:c.616G>A

Your query was ambiguous. Multiple possible variants found:

• chr16-722465-G-A
• chr16-722465-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_023933.3(ANTKMT):​c.616G>A​(p.Gly206Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. 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. G206E) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: ANTKMT NM_023933.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400

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]

CCDC78 (HGNC:14153): (coiled-coil domain containing 78) Involved in de novo centriole assembly involved in multi-ciliated epithelial cell differentiation and skeletal muscle contraction. Located in several cellular components, including centriole; deuterosome; and sarcolemma. Implicated in centronuclear myopathy 4. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.08839765).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANTKMT	NM_023933.3	c.616G>A	p.Gly206Arg	missense_variant	Exon 5 of 5	ENST00000569529.6	NP_076422.1
CCDC78	NM_001378030.1	c.*213C>T		downstream_gene_variant		ENST00000345165.10	NP_001364959.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANTKMT	ENST00000569529.6	c.616G>A	p.Gly206Arg	missense_variant	Exon 5 of 5	1	NM_023933.3	ENSP00000454380.1
CCDC78	ENST00000345165.10	c.*213C>T		downstream_gene_variant		5	NM_001378030.1	ENSP00000316851.5

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 46

GnomAD4 genome Cov.: 33

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.091
BayesDel_addAF	Benign	-0.29	T
BayesDel_noAF	Benign	-0.65
CADD	Benign	12
DANN	Benign	0.88
DEOGEN2	Benign	0.018	T;T
Eigen	Benign	-0.65
Eigen_PC	Benign	-0.88
FATHMM_MKL	Benign	0.044	N
LIST_S2	Benign	0.55	T;T
M_CAP	Benign	0.0031	T
MetaRNN	Benign	0.088	T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.97	L;.
PrimateAI	Benign	0.38	T
PROVEAN	Benign	0.49	N;N
REVEL	Benign	0.063
Sift	Benign	0.52	T;T
Sift4G	Benign	0.091	T;T
Polyphen		0.99	D;.
Vest4		0.10
MutPred		0.23		Loss of loop (P = 0.0288);.;
MVP		0.22
MPC		0.096
ClinPred		0.17	T
GERP RS		-1.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.031
gMVP		0.41

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: rs760194287; hg19: chr16-772465;