14-58223688-A-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_018477.3(ACTR10):​c.701A>T​(p.Asp234Val) variant causes a missense change. The variant allele was found at a frequency of 0.000531 in 1,611,634 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00032 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00055 ( 1 hom. )

Consequence

ACTR10
NM_018477.3 missense

Scores

3
10
6

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.75
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

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=0.20453939).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ACTR10NM_018477.3 linkuse as main transcriptc.701A>T p.Asp234Val missense_variant 9/13 ENST00000254286.9 NP_060947.1
ACTR10XM_011536960.2 linkuse as main transcriptc.722A>T p.Asp241Val missense_variant 9/13 XP_011535262.1
ACTR10XM_011536961.2 linkuse as main transcriptc.665A>T p.Asp222Val missense_variant 8/12 XP_011535263.1
ACTR10XM_047431587.1 linkuse as main transcriptc.128A>T p.Asp43Val missense_variant 4/8 XP_047287543.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ACTR10ENST00000254286.9 linkuse as main transcriptc.701A>T p.Asp234Val missense_variant 9/131 NM_018477.3 ENSP00000254286 P1

Frequencies

GnomAD3 genomes
AF:
0.000323
AC:
49
AN:
151540
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000171
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000618
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000221
AC:
55
AN:
248594
Hom.:
0
AF XY:
0.000216
AC XY:
29
AN XY:
134384
show subpopulations
Gnomad AFR exome
AF:
0.0000627
Gnomad AMR exome
AF:
0.0000292
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000461
Gnomad OTH exome
AF:
0.000165
GnomAD4 exome
AF:
0.000552
AC:
806
AN:
1460094
Hom.:
1
Cov.:
30
AF XY:
0.000547
AC XY:
397
AN XY:
726270
show subpopulations
Gnomad4 AFR exome
AF:
0.0000898
Gnomad4 AMR exome
AF:
0.0000225
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.0000187
Gnomad4 NFE exome
AF:
0.000692
Gnomad4 OTH exome
AF:
0.000531
GnomAD4 genome
AF:
0.000323
AC:
49
AN:
151540
Hom.:
0
Cov.:
32
AF XY:
0.000270
AC XY:
20
AN XY:
74000
show subpopulations
Gnomad4 AFR
AF:
0.000171
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000618
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000581
Hom.:
0
Bravo
AF:
0.000264
TwinsUK
AF:
0.000809
AC:
3
ALSPAC
AF:
0.000519
AC:
2
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000233
AC:
2
ExAC
AF:
0.000173
AC:
21
EpiCase
AF:
0.000382
EpiControl
AF:
0.000417

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsMar 31, 2024The c.701A>T (p.D234V) alteration is located in exon 9 (coding exon 9) of the ACTR10 gene. This alteration results from a A to T substitution at nucleotide position 701, causing the aspartic acid (D) at amino acid position 234 to be replaced by a valine (V). 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
0.17
BayesDel_addAF
Uncertain
0.080
D
BayesDel_noAF
Pathogenic
0.25
CADD
Benign
22
DANN
Uncertain
0.99
DEOGEN2
Uncertain
0.62
D
Eigen
Uncertain
0.21
Eigen_PC
Uncertain
0.30
FATHMM_MKL
Pathogenic
0.97
D
LIST_S2
Uncertain
0.95
D
M_CAP
Uncertain
0.11
D
MetaRNN
Benign
0.20
T
MetaSVM
Benign
-0.88
T
MutationAssessor
Uncertain
2.6
M
MutationTaster
Benign
1.0
D
PrimateAI
Uncertain
0.52
T
PROVEAN
Benign
-1.7
N
REVEL
Pathogenic
0.68
Sift
Uncertain
0.0040
D
Sift4G
Benign
0.12
T
Polyphen
0.16
B
Vest4
0.39
MVP
0.97
MPC
0.49
ClinPred
0.083
T
GERP RS
4.8
Varity_R
0.34
gMVP
0.70

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs200823272; hg19: chr14-58690406; API