chr10-114465758-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_002313.7(ABLIM1):c.1381T>G(p.Tyr461Asp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,614,104 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000014 ( 1 hom. )
Consequence
ABLIM1
NM_002313.7 missense
NM_002313.7 missense
Scores
7
7
3
Clinical Significance
Conservation
PhyloP100: 9.21
Genes affected
ABLIM1 (HGNC:78): (actin binding LIM protein 1) This gene encodes a LIM zinc-binding domain-containing protein that binds to actin filaments and mediates interactions between actin and cytoplasmic targets. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jun 2017]
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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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABLIM1 | NM_002313.7 | c.1381T>G | p.Tyr461Asp | missense_variant | 12/23 | ENST00000533213.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABLIM1 | ENST00000533213.7 | c.1381T>G | p.Tyr461Asp | missense_variant | 12/23 | 5 | NM_002313.7 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152128Hom.: 0 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0000757 AC: 19AN: 251118Hom.: 1 AF XY: 0.0000442 AC XY: 6AN XY: 135762
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GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461858Hom.: 1 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727226
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GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152246Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74450
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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 submitter | clinical testing | Ambry Genetics | Dec 07, 2021 | The c.1381T>G (p.Y461D) alteration is located in exon 12 (coding exon 12) of the ABLIM1 gene. This alteration results from a T to G substitution at nucleotide position 1381, causing the tyrosine (Y) at amino acid position 461 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Uncertain
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Pathogenic
D;D;D;D;D;D;D;D;D;D;D
M_CAP
Benign
D
MetaRNN
Uncertain
D;D;D;D;D;D;D;D;D;D;D
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D;D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;.;D;.;.;.;D;.;.;D;D
REVEL
Uncertain
Sift
Uncertain
D;.;D;.;.;.;T;.;.;D;D
Sift4G
Uncertain
D;D;D;D;D;D;D;D;.;D;.
Polyphen
D;.;D;.;D;.;.;D;.;.;.
Vest4
MutPred
0.39
.;.;.;.;.;.;.;Loss of phosphorylation at Y461 (P = 0.0199);.;.;.;
MVP
MPC
1.5
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at