chr19-16896552-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_015692.5(CPAMD8):​c.5179G>A​(p.Asp1727Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00855 in 1,502,024 control chromosomes in the GnomAD database, including 535 homozygotes. In-silico tool predicts a benign outcome for this variant. 9/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.035 ( 261 hom., cov: 31)
Exomes 𝑓: 0.0056 ( 274 hom. )

Consequence

CPAMD8
NM_015692.5 missense

Scores

1
1
11

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.932
Variant links:
Genes affected
CPAMD8 (HGNC:23228): (C3 and PZP like alpha-2-macroglobulin domain containing 8) This gene encodes a member of the protease inhibitor I39 (alpha-2-macroglobulin) family of proteins. These proteins are important in innate and acquired immunity. The encoded protein is membrane-associated and proteolytically processed to generate two chains. Mutations in this gene cause a form of anterior segment dysgenesis, a developmental disorder of the eye. [provided by RefSeq, May 2017]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.0016382039).
BP6
Variant 19-16896552-C-T is Benign according to our data. Variant chr19-16896552-C-T is described in ClinVar as [Benign]. Clinvar id is 1248916.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-16896552-C-T is described in Lovd as [Likely_benign].
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CPAMD8NM_015692.5 linkuse as main transcriptc.5179G>A p.Asp1727Asn missense_variant 40/42 ENST00000443236.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CPAMD8ENST00000443236.7 linkuse as main transcriptc.5179G>A p.Asp1727Asn missense_variant 40/421 NM_015692.5 P2Q8IZJ3-1

Frequencies

GnomAD3 genomes
AF:
0.0348
AC:
5296
AN:
152104
Hom.:
259
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.108
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0206
Gnomad ASJ
AF:
0.0210
Gnomad EAS
AF:
0.0523
Gnomad SAS
AF:
0.00497
Gnomad FIN
AF:
0.0000942
Gnomad MID
AF:
0.0223
Gnomad NFE
AF:
0.00115
Gnomad OTH
AF:
0.0311
GnomAD3 exomes
AF:
0.0137
AC:
1404
AN:
102614
Hom.:
49
AF XY:
0.0121
AC XY:
689
AN XY:
57048
show subpopulations
Gnomad AFR exome
AF:
0.143
Gnomad AMR exome
AF:
0.0113
Gnomad ASJ exome
AF:
0.0203
Gnomad EAS exome
AF:
0.0661
Gnomad SAS exome
AF:
0.00409
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00188
Gnomad OTH exome
AF:
0.00866
GnomAD4 exome
AF:
0.00558
AC:
7533
AN:
1349812
Hom.:
274
Cov.:
32
AF XY:
0.00516
AC XY:
3432
AN XY:
665168
show subpopulations
Gnomad4 AFR exome
AF:
0.114
Gnomad4 AMR exome
AF:
0.0126
Gnomad4 ASJ exome
AF:
0.0226
Gnomad4 EAS exome
AF:
0.0444
Gnomad4 SAS exome
AF:
0.00427
Gnomad4 FIN exome
AF:
0.0000304
Gnomad4 NFE exome
AF:
0.000677
Gnomad4 OTH exome
AF:
0.0138
GnomAD4 genome
AF:
0.0349
AC:
5308
AN:
152212
Hom.:
261
Cov.:
31
AF XY:
0.0335
AC XY:
2492
AN XY:
74416
show subpopulations
Gnomad4 AFR
AF:
0.108
Gnomad4 AMR
AF:
0.0205
Gnomad4 ASJ
AF:
0.0210
Gnomad4 EAS
AF:
0.0526
Gnomad4 SAS
AF:
0.00518
Gnomad4 FIN
AF:
0.0000942
Gnomad4 NFE
AF:
0.00115
Gnomad4 OTH
AF:
0.0307
Alfa
AF:
0.00390
Hom.:
2
Bravo
AF:
0.0406
ExAC
AF:
0.00641
AC:
139
Asia WGS
AF:
0.0240
AC:
84
AN:
3474

ClinVar

Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:3
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 11, 2024- -
Benign, criteria provided, single submitterclinical testingGeneDxMay 04, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.20
BayesDel_addAF
Benign
-0.75
T
BayesDel_noAF
Benign
-0.73
CADD
Benign
15
DANN
Uncertain
0.98
Eigen
Benign
-0.65
Eigen_PC
Benign
-0.72
FATHMM_MKL
Benign
0.59
D
LIST_S2
Benign
0.85
T;T
MetaRNN
Benign
0.0016
T;T
MetaSVM
Benign
-1.1
T
MutationTaster
Benign
0.91
N
PrimateAI
Pathogenic
0.83
D
Sift4G
Benign
0.29
T;.
Vest4
0.15
MPC
1.3
ClinPred
0.017
T
GERP RS
1.1

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: rs10418195; hg19: chr19-17007363; API