4-8020300-C-T
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001130083.2(ABLIM2):c.1271G>A(p.Ser424Asn) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,238 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
ABLIM2
NM_001130083.2 missense
NM_001130083.2 missense
Scores
6
11
Clinical Significance
Conservation
PhyloP100: 6.94
Genes affected
ABLIM2 (HGNC:19195): (actin binding LIM protein family member 2) Predicted to enable actin filament binding activity. Predicted to be involved in lamellipodium assembly. Predicted to act upstream of or within positive regulation of transcription by RNA polymerase II. Located in actin cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.34994653).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABLIM2 | NM_001130083.2 | c.1271G>A | p.Ser424Asn | missense_variant | 13/21 | ENST00000447017.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABLIM2 | ENST00000447017.7 | c.1271G>A | p.Ser424Asn | missense_variant | 13/21 | 1 | NM_001130083.2 | P4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
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32
GnomAD3 exomes AF: 0.00000405 AC: 1AN: 246706Hom.: 0 AF XY: 0.00000744 AC XY: 1AN XY: 134426
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GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461238Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726848
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GnomAD4 genome Cov.: 32
GnomAD4 genome
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32
ExAC
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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 | Jun 10, 2022 | The c.1271G>A (p.S424N) alteration is located in exon 13 (coding exon 13) of the ABLIM2 gene. This alteration results from a G to A substitution at nucleotide position 1271, causing the serine (S) at amino acid position 424 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;T;T;D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D;D;D;D;D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;.;N
REVEL
Benign
Sift
Benign
T;T;T;.;T
Sift4G
Benign
T;T;T;T;T
Polyphen
0.91, 0.97
.;P;D;.;.
Vest4
MutPred
0.21
.;Gain of glycosylation at Y386 (P = 0.0016);Gain of glycosylation at Y386 (P = 0.0016);.;.;
MVP
MPC
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