14-58215244-C-A

Variant names:

• chr14-58215244-C-A
• NM_018477.3:c.558C>A

Variant summary

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

The NM_018477.3(ACTR10):​c.558C>A​(p.Asp186Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 31)
• Consequence: ACTR10 NM_018477.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.262

Genes affected

ACTR10 (HGNC:17372): (actin related protein 10) Predicted to be involved in retrograde axonal transport of mitochondrion. Predicted to be located in cytosol; extracellular region; and secretory granule. Predicted to be part of dynactin complex. [provided by Alliance of Genome Resources, Apr 2022]

ARMH4 (HGNC:19846): (armadillo like helical domain containing 4) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACTR10	NM_018477.3	c.558C>A	p.Asp186Glu	missense_variant	Exon 7 of 13	ENST00000254286.9	NP_060947.1
ACTR10	XM_011536960.2	c.558C>A	p.Asp186Glu	missense_variant	Exon 7 of 13		XP_011535262.1
ACTR10	XM_011536961.2	c.558C>A	p.Asp186Glu	missense_variant	Exon 7 of 12		XP_011535263.1
ACTR10	XM_047431587.1	c.-37C>A		5_prime_UTR_variant	Exon 2 of 8		XP_047287543.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACTR10	ENST00000254286.9	c.558C>A	p.Asp186Glu	missense_variant	Exon 7 of 13	1	NM_018477.3	ENSP00000254286.4
ACTR10	ENST00000554402.6	n.555C>A		non_coding_transcript_exon_variant	Exon 7 of 14	1		ENSP00000477173.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 31

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

May 23, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.558C>A (p.D186E) alteration is located in exon 7 (coding exon 7) of the ACTR10 gene. This alteration results from a C to A substitution at nucleotide position 558, causing the aspartic acid (D) at amino acid position 186 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.24
BayesDel_addAF	Pathogenic	0.18	D
BayesDel_noAF	Uncertain	0.020
CADD	Benign	13
DANN	Uncertain	0.99
DEOGEN2	Benign	0.28	T
Eigen	Benign	-0.51
Eigen_PC	Benign	-0.34
FATHMM_MKL	Uncertain	0.93	D
LIST_S2	Benign	0.85	T
M_CAP	Benign	0.072	D
MetaRNN	Uncertain	0.52	D
MetaSVM	Uncertain	-0.22	T
MutationAssessor	Benign	1.6	L
PrimateAI	Uncertain	0.73	T
PROVEAN	Benign	-0.15	N
REVEL	Uncertain	0.49
Sift	Benign	0.29	T
Sift4G	Benign	0.35	T
Polyphen		0.021	B
Vest4		0.73
MutPred		0.53		Gain of disorder (P = 0.0715);
MVP		0.79
MPC		0.29
ClinPred		0.35	T
GERP RS		3.9
Varity_R		0.079
gMVP		0.41

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr14-58681962;