11-101895062-C-G
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_178127.5(ANGPTL5):c.664G>C(p.Glu222Gln) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00000255 in 1,569,484 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000021 ( 1 hom. )
Consequence
ANGPTL5
NM_178127.5 missense, splice_region
NM_178127.5 missense, splice_region
Scores
10
7
2
Clinical Significance
Conservation
PhyloP100: 7.06
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.973
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANGPTL5 | NM_178127.5 | c.664G>C | p.Glu222Gln | missense_variant, splice_region_variant | 8/9 | ENST00000334289.7 | |
ANGPTL5 | XM_011542735.4 | c.469G>C | p.Glu157Gln | missense_variant, splice_region_variant | 6/7 | ||
ANGPTL5 | XM_017017466.3 | c.244G>C | p.Glu82Gln | missense_variant, splice_region_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANGPTL5 | ENST00000334289.7 | c.664G>C | p.Glu222Gln | missense_variant, splice_region_variant | 8/9 | 1 | NM_178127.5 | P1 | |
ANGPTL5 | ENST00000534527.1 | c.469G>C | p.Glu157Gln | missense_variant, splice_region_variant | 5/5 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 151978Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.00000212 AC: 3AN: 1417506Hom.: 1 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 706074
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GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 151978Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74216
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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 | Jan 26, 2023 | The c.664G>C (p.E222Q) alteration is located in exon 8 (coding exon 7) of the ANGPTL5 gene. This alteration results from a G to C substitution at nucleotide position 664, causing the glutamic acid (E) at amino acid position 222 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D
MetaSVM
Pathogenic
D
MutationAssessor
Pathogenic
H;.
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D
REVEL
Pathogenic
Sift
Uncertain
D;D
Sift4G
Uncertain
D;D
Polyphen
D;.
Vest4
MutPred
Gain of MoRF binding (P = 0.0679);.;
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