1-147655173-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_016361.5(ACP6):​c.635G>A​(p.Arg212Lys) 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. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

ACP6
NM_016361.5 missense

Scores

17

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.0740
Variant links:
Genes affected
ACP6 (HGNC:29609): (acid phosphatase 6, lysophosphatidic) This gene encodes a member of the histidine acid phosphatase protein family. The encoded protein hydrolyzes lysophosphatidic acid, which is involved in G protein-coupled receptor signaling, lipid raft modulation, and in balancing lipid composition within the cell. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2016]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.056426138).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ACP6NM_016361.5 linkuse as main transcriptc.635G>A p.Arg212Lys missense_variant 5/10 ENST00000583509.7 NP_057445.4 Q9NPH0-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ACP6ENST00000583509.7 linkuse as main transcriptc.635G>A p.Arg212Lys missense_variant 5/101 NM_016361.5 ENSP00000463574.1 Q9NPH0-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
30
GnomAD4 genome
Cov.:
32

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 GeneticsAug 09, 2021The c.635G>A (p.R212K) alteration is located in exon 5 (coding exon 5) of the ACP6 gene. This alteration results from a G to A substitution at nucleotide position 635, causing the arginine (R) at amino acid position 212 to be replaced by a lysine (K). 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
0.085
BayesDel_addAF
Benign
-0.33
T
BayesDel_noAF
Benign
-0.72
CADD
Benign
4.6
DANN
Benign
0.76
DEOGEN2
Benign
0.039
T;.;.
Eigen
Benign
-1.1
Eigen_PC
Benign
-1.0
FATHMM_MKL
Benign
0.026
N
LIST_S2
Benign
0.62
T;T;T
M_CAP
Benign
0.0025
T
MetaRNN
Benign
0.056
T;T;T
MetaSVM
Benign
-0.95
T
MutationAssessor
Benign
0.43
N;N;.
PrimateAI
Benign
0.34
T
REVEL
Benign
0.13
Sift4G
Benign
1.0
T;T;T
Polyphen
0.0040
B;B;.
Vest4
0.059
MutPred
0.53
Gain of methylation at R212 (P = 0.0062);Gain of methylation at R212 (P = 0.0062);.;
MVP
0.23
ClinPred
0.094
T
GERP RS
-0.95
Varity_R
0.043
gMVP
0.35

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-147127288; API