rs6512158

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015692.5(CPAMD8):​c.486+741T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,022 control chromosomes in the GnomAD database, including 4,335 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.21 ( 4335 hom., cov: 31)

Consequence

CPAMD8
NM_015692.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.273
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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CPAMD8NM_015692.5 linkuse as main transcriptc.486+741T>G intron_variant ENST00000443236.7 NP_056507.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CPAMD8ENST00000443236.7 linkuse as main transcriptc.486+741T>G intron_variant 1 NM_015692.5 ENSP00000402505.3 Q8IZJ3-1
CPAMD8ENST00000291440.4 linkuse as main transcriptn.486+741T>G intron_variant 1 ENSP00000291440.4 F8W7D1
CPAMD8ENST00000651564.2 linkuse as main transcriptc.486+741T>G intron_variant ENSP00000498697.2 Q8IZJ3-2A0A494C0S9
ENSG00000268985ENST00000595134.1 linkuse as main transcriptn.315+1220A>C intron_variant 2

Frequencies

GnomAD3 genomes
AF:
0.210
AC:
31928
AN:
151904
Hom.:
4314
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.387
Gnomad AMI
AF:
0.179
Gnomad AMR
AF:
0.131
Gnomad ASJ
AF:
0.0939
Gnomad EAS
AF:
0.115
Gnomad SAS
AF:
0.0967
Gnomad FIN
AF:
0.191
Gnomad MID
AF:
0.123
Gnomad NFE
AF:
0.147
Gnomad OTH
AF:
0.180
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.210
AC:
31987
AN:
152022
Hom.:
4335
Cov.:
31
AF XY:
0.208
AC XY:
15493
AN XY:
74310
show subpopulations
Gnomad4 AFR
AF:
0.387
Gnomad4 AMR
AF:
0.131
Gnomad4 ASJ
AF:
0.0939
Gnomad4 EAS
AF:
0.115
Gnomad4 SAS
AF:
0.0957
Gnomad4 FIN
AF:
0.191
Gnomad4 NFE
AF:
0.147
Gnomad4 OTH
AF:
0.178
Alfa
AF:
0.151
Hom.:
2499
Bravo
AF:
0.215
Asia WGS
AF:
0.128
AC:
445
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.82
DANN
Benign
0.55

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: rs6512158; hg19: chr19-17121533; API