Genetic Variant C4BPAP1:n.207180855A>G (chr1-207180855-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.0894 in 152,122 control chromosomes in the GnomAD database, including 1,456 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 0.089 ( 1456 hom., cov: 32)

Consequence

C4BPAP1
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.906

Publications

1 publications found

Variant links:

Genes affected

C4BPAP1 (HGNC:1326): (C4BPA pseudogene 1)

C4BPAP1 links:

ENSG00000243636 (HGNC:):

ENSG00000243636 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
C4BPAP1		n.207180855A>G	intragenic_variant
LOC107985251	XR_007066837.1 link	n.445-25797T>C	intron_variant	Intron 1 of 3
LOC107985251	XR_007066838.1 link	n.445-46075T>C	intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
C4BPAP1	ENST00000415474.1 link	n.1301-520A>G	intron_variant	Intron 8 of 10	6
ENSG00000243636	ENST00000442684.2 link	n.250-520A>G	intron_variant	Intron 1 of 3	3
ENSG00000296591	ENST00000740658.1 link	n.117-46075T>C	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0891

AC:

13550

AN:

152004

Hom.:

1447

Cov.:

show subpopulations

Gnomad AFR

AF:

0.258

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0460

Gnomad ASJ

AF:

0.0190

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00809

Gnomad FIN

AF:

0.0362

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0226

Gnomad OTH

AF:

0.0745

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0894

AC:

13597

AN:

152122

Hom.:

1456

Cov.:

AF XY:

0.0871

AC XY:

6476

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.258

AC:

10701

AN:

41428

American (AMR)

AF:

0.0459

AC:

702

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0190

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5176

South Asian (SAS)

AF:

0.00789

AC:

AN:

4818

European-Finnish (FIN)

AF:

0.0362

AC:

384

AN:

10600

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0226

AC:

1536

AN:

68016

Other (OTH)

AF:

0.0737

AC:

156

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

527

1054

1580

2107

2634

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

132

264

396

528

660

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0525

Hom.:

104

Bravo

AF:

0.0992

Asia WGS

AF:

0.0310

AC:

110

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

0.86

(source)

DANN

Benign

0.51

PhyloP100

-0.91

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over