3-169767599-C-T

Variant summary

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

The NM_032487.5(ACTRT3):​c.952G>A​(p.Ala318Thr) 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. A318S) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)

Consequence

ACTRT3
NM_032487.5 missense

Scores

10
9

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.16
Variant links:
Genes affected
ACTRT3 (HGNC:24022): (actin related protein T3) Predicted to be located in male germ cell nucleus. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

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
ACTRT3NM_032487.5 linkc.952G>A p.Ala318Thr missense_variant Exon 2 of 2 ENST00000330368.3 NP_115876.3 Q9BYD9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ACTRT3ENST00000330368.3 linkc.952G>A p.Ala318Thr missense_variant Exon 2 of 2 1 NM_032487.5 ENSP00000333037.1 Q9BYD9

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD3 exomes
AF:
0.00000398
AC:
1
AN:
251308
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
135818
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.16
BayesDel_addAF
Benign
0.011
T
BayesDel_noAF
Benign
-0.13
CADD
Uncertain
23
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.43
T
Eigen
Benign
0.088
Eigen_PC
Benign
0.021
FATHMM_MKL
Uncertain
0.86
D
LIST_S2
Benign
0.68
T
M_CAP
Benign
0.066
D
MetaRNN
Uncertain
0.55
D
MetaSVM
Uncertain
0.79
D
MutationAssessor
Uncertain
2.2
M
PrimateAI
Benign
0.29
T
PROVEAN
Uncertain
-2.4
N
REVEL
Uncertain
0.43
Sift
Uncertain
0.0010
D
Sift4G
Uncertain
0.029
D
Polyphen
0.71
P
Vest4
0.15
MutPred
0.74
Loss of catalytic residue at A318 (P = 0.0841);
MVP
0.51
MPC
0.33
ClinPred
0.95
D
GERP RS
4.3
Varity_R
0.32
gMVP
0.15

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: rs1202342289; hg19: chr3-169485387; API