Variant chr19-16892978-T-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_015692.5(CPAMD8):c.*130A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.542 in 766,154 control chromosomes in the GnomAD database, including 115,631 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.59 ( 27645 hom., cov: 32)

Exomes 𝑓: 0.53 ( 87986 hom. )

Consequence

CPAMD8
NM_015692.5 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.58

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]

CPAMD8 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

BP6

Variant 19-16892978-T-G is Benign according to our data. Variant chr19-16892978-T-G is described in ClinVar as [Benign]. Clinvar id is 1240872.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CPAMD8	NM_015692.5 linkuse as main transcript	c.*130A>C		3_prime_UTR_variant	42/42	ENST00000443236.7

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPAMD8	ENST00000443236.7 linkuse as main transcript	c.*130A>C	3_prime_UTR_variant	42/42	1	NM_015692.5	P2	Q8IZJ3-1
CPAMD8	ENST00000651564.2 linkuse as main transcript	c.*1438A>C	3_prime_UTR_variant	42/42			A2	Q8IZJ3-2
CPAMD8	ENST00000596224.5 linkuse as main transcript	n.2097A>C	non_coding_transcript_exon_variant	3/3	2
CPAMD8	ENST00000600235.5 linkuse as main transcript	n.3462A>C	non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes

AF:

0.593

AC:

90132

AN:

151940

Hom.:

27591

Cov.:

show subpopulations

Gnomad AFR

AF:

0.751

Gnomad AMI

AF:

0.578

Gnomad AMR

AF:

0.576

Gnomad ASJ

AF:

0.570

Gnomad EAS

AF:

0.321

Gnomad SAS

AF:

0.540

Gnomad FIN

AF:

0.563

Gnomad MID

AF:

0.649

Gnomad NFE

AF:

0.531

Gnomad OTH

AF:

0.608

GnomAD3 exomes

AF:

0.533

AC:

127013

AN:

238208

Hom.:

34819

AF XY:

0.535

AC XY:

69778

AN XY:

130342

show subpopulations

Gnomad AFR exome

AF:

0.759

Gnomad AMR exome

AF:

0.524

Gnomad ASJ exome

AF:

0.567

Gnomad EAS exome

AF:

0.324

Gnomad SAS exome

AF:

0.549

Gnomad FIN exome

AF:

0.542

Gnomad NFE exome

AF:

0.529

Gnomad OTH exome

AF:

0.552

GnomAD4 exome

AF:

0.529

AC:

325088

AN:

614096

Hom.:

87986

Cov.:

AF XY:

0.532

AC XY:

178020

AN XY:

334760

show subpopulations

Gnomad4 AFR exome

AF:

0.752

Gnomad4 AMR exome

AF:

0.527

Gnomad4 ASJ exome

AF:

0.563

Gnomad4 EAS exome

AF:

0.311

Gnomad4 SAS exome

AF:

0.554

Gnomad4 FIN exome

AF:

0.538

Gnomad4 NFE exome

AF:

0.531

Gnomad4 OTH exome

AF:

0.544

GnomAD4 genome

AF:

0.594

AC:

90258

AN:

152058

Hom.:

27645

Cov.:

AF XY:

0.593

AC XY:

44088

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.751

Gnomad4 AMR

AF:

0.576

Gnomad4 ASJ

AF:

0.570

Gnomad4 EAS

AF:

0.321

Gnomad4 SAS

AF:

0.541

Gnomad4 FIN

AF:

0.563

Gnomad4 NFE

AF:

0.531

Gnomad4 OTH

AF:

0.608

Alfa

AF:

0.537

Hom.:

35194

Bravo

AF:

0.601

Asia WGS

AF:

0.477

AC:

1658

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 10, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.043

DANN

Benign

0.49

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over