GeneBe

7-128877202-G-T

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001366122.1(KCP):​c.4728C>A​(p.Cys1576*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000226 in 1,329,572 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
Exomes 𝑓: 0.0000023 ( 0 hom. )

Consequence

KCP
NM_001366122.1 stop_gained

Scores

4

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.13

Publications

0 publications found
Variant links:
Genes affected
KCP (HGNC:17585): (kielin cysteine rich BMP regulator) Predicted to act upstream of or within hematopoietic progenitor cell differentiation and positive regulation of BMP signaling pathway. Predicted to be located in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
KCPNM_001366122.1 linkc.4728C>A p.Cys1576* stop_gained Exon 40 of 40 ENST00000610776.5 NP_001353051.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
KCPENST00000610776.5 linkc.4728C>A p.Cys1576* stop_gained Exon 40 of 40 5 NM_001366122.1 ENSP00000479679.1 A0A087WVT8

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.00000226
AC:
3
AN:
1329572
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
649672
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
28742
American (AMR)
AF:
0.00
AC:
0
AN:
21648
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
20928
East Asian (EAS)
AF:
0.00
AC:
0
AN:
35082
South Asian (SAS)
AF:
0.00
AC:
0
AN:
68312
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
46520
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4954
European-Non Finnish (NFE)
AF:
0.00000286
AC:
3
AN:
1048512
Other (OTH)
AF:
0.00
AC:
0
AN:
54874
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
33
Alfa
AF:
0.00
Hom.:
0
Bravo
AF:
0.0000113

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.16
T
BayesDel_noAF
Benign
-0.46
CADD
Uncertain
24
DANN
Benign
0.70
FATHMM_MKL
Benign
0.18
N
PhyloP100
-1.1
Vest4
0.58
GERP RS
-3.8
Mutation Taster
=99/1
polymorphism

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs567302036; hg19: chr7-128517256; API