rs898690659

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2

The NM_001833.4(CLTA):​c.212G>A​(p.Gly71Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000438 in 1,370,482 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000044 ( 0 hom. )

Consequence

CLTA
NM_001833.4 missense

Scores

3
16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.533
Variant links:
Genes affected
CLTA (HGNC:2090): (clathrin light chain A) Clathrin is a large, soluble protein composed of heavy and light chains. It functions as the main structural component of the lattice-type cytoplasmic face of coated pits and vesicles which entrap specific macromolecules during receptor-mediated endocytosis. This gene encodes one of two clathrin light chain proteins which are believed to function as regulatory elements. Alternative splicing results in multiple transcript variants. Related pseudogenes have been identified on chromosomes 8 and 12. [provided by RefSeq, May 2010]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.08534351).
BS2
High AC in GnomAdExome4 at 6 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CLTANM_001833.4 linkc.212G>A p.Gly71Asp missense_variant Exon 1 of 5 ENST00000345519.10 NP_001824.1 P09496-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CLTAENST00000345519.10 linkc.212G>A p.Gly71Asp missense_variant Exon 1 of 5 1 NM_001833.4 ENSP00000242284.6 P09496-2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.0000168
AC:
2
AN:
118970
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
65816
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:
0.00
Gnomad FIN exome
AF:
0.000135
Gnomad NFE exome
AF:
0.0000218
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000438
AC:
6
AN:
1370482
Hom.:
0
Cov.:
31
AF XY:
0.00000296
AC XY:
2
AN XY:
675986
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.000102
Gnomad4 NFE exome
AF:
0.00000186
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
Bravo
AF:
0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.11
BayesDel_addAF
Benign
-0.076
T
BayesDel_noAF
Benign
-0.31
CADD
Benign
18
DANN
Uncertain
0.99
DEOGEN2
Benign
0.18
.;T;.;.;.;T;.;.
Eigen
Benign
-0.40
Eigen_PC
Benign
-0.21
FATHMM_MKL
Benign
0.64
D
LIST_S2
Uncertain
0.93
D;T;T;T;.;.;D;T
M_CAP
Benign
0.0098
T
MetaRNN
Benign
0.085
T;T;T;T;T;T;T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.7
L;L;L;L;L;L;.;L
PrimateAI
Uncertain
0.71
T
PROVEAN
Benign
0.050
N;N;N;N;N;N;N;N
REVEL
Benign
0.054
Sift
Benign
0.20
T;T;T;T;T;T;T;T
Sift4G
Benign
0.13
T;T;T;T;T;T;T;T
Polyphen
0.0010, 0.0020
.;B;.;B;.;B;.;B
Vest4
0.23
MutPred
0.32
Gain of helix (P = 0.062);Gain of helix (P = 0.062);Gain of helix (P = 0.062);Gain of helix (P = 0.062);Gain of helix (P = 0.062);Gain of helix (P = 0.062);Gain of helix (P = 0.062);Gain of helix (P = 0.062);
MVP
0.38
MPC
0.69
ClinPred
0.082
T
GERP RS
3.5
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.2
Varity_R
0.13
gMVP
0.53

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: rs898690659; hg19: chr9-36191265; API