NM_001164458.2:c.479A>C

Variant names:

• chr7-150284838-T-G
• rs542899681
• NM_001164458.2:c.479A>C

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001164458.2(ACTR3C):​c.479A>C​(p.Asn160Thr) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts 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. N160I) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ACTR3C NM_001164458.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.58
• Publications: 0 publications found

Genes affected

ACTR3C (HGNC:37282): (actin related protein 3C) Predicted to enable ATP binding activity. Predicted to contribute to actin filament binding activity. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.41601357).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACTR3C	NM_001164458.2	c.479A>C	p.Asn160Thr	missense_variant	Exon 6 of 8	ENST00000683684.1	NP_001157930.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACTR3C	ENST00000683684.1	c.479A>C	p.Asn160Thr	missense_variant	Exon 6 of 8		NM_001164458.2	ENSP00000507618.1
ACTR3C	ENST00000252071.8	c.479A>C	p.Asn160Thr	missense_variant	Exon 6 of 8	1		ENSP00000252071.4
ACTR3C	ENST00000478393.5	c.473A>C	p.Asn158Thr	missense_variant	Exon 5 of 6	1		ENSP00000417426.1
ACTR3C	ENST00000539352.5	c.479A>C	p.Asn160Thr	missense_variant	Exon 5 of 5	5		ENSP00000440990.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.19
BayesDel_addAF	Benign	-0.13	T
BayesDel_noAF	Benign	-0.43
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Benign	0.054	.;T;.
Eigen	Uncertain	0.43
Eigen_PC	Uncertain	0.29
FATHMM_MKL	Uncertain	0.92	D
LIST_S2	Pathogenic	0.99	D;D;D
M_CAP	Benign	0.0019	T
MetaRNN	Benign	0.42	T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Pathogenic	3.1	.;M;.
PhyloP100		5.6
PROVEAN	Uncertain	-2.7	D;D;D
REVEL	Benign	0.17
Sift	Benign	0.042	D;D;D
Sift4G	Uncertain	0.036	D;D;D
Polyphen		1.0	.;D;.
Vest4		0.65, 0.65
MutPred		0.42		.;Gain of phosphorylation at N160 (P = 0.032);Gain of phosphorylation at N160 (P = 0.032);
MVP		0.45
MPC		0.65
ClinPred		0.98	D
GERP RS		2.2
Varity_R		0.31
gMVP		0.43
Mutation Taster		=67/33	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs542899681; hg19: chr7-149981927;