10-101062803-A-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_030929.5(KAZALD1):c.211A>T(p.Arg71Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00176 in 1,577,584 control chromosomes in the GnomAD database, including 53 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0092 ( 20 hom., cov: 33)
Exomes 𝑓: 0.00096 ( 33 hom. )
Consequence
KAZALD1
NM_030929.5 missense
NM_030929.5 missense
Scores
2
16
Clinical Significance
Conservation
PhyloP100: -0.252
Genes affected
KAZALD1 (HGNC:25460): (Kazal type serine peptidase inhibitor domain 1) This gene encodes a secreted member of the insulin growth factor-binding protein (IGFBP) superfamily. The protein contains an insulin growth factor-binding domain in its N-terminal region, a Kazal-type serine protease inhibitor and follistatin-like domain in its central region, and an immunoglobulin-like domain in its C-terminal region. Studies of the mouse ortholog suggest that this protein may function in bone development and bone regeneration. This gene is hypomethylated and over-expressed in high-grade glioma compared to low-grade glioma, and thus the hypomethylated gene may be associated with cell proliferation and the shorter survival of patients with high-grade glioma. It is also one of numerous genes found to be deleted in a novel 5.54 Mb interstitial deletion, which is associated with multiple congenital anomalies. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0037122667).
BP6
?
Variant 10-101062803-A-T is Benign according to our data. Variant chr10-101062803-A-T is described in ClinVar as [Benign]. Clinvar id is 716217.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00921 (1402/152290) while in subpopulation AFR AF= 0.0327 (1358/41564). AF 95% confidence interval is 0.0312. There are 20 homozygotes in gnomad4. There are 641 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 19 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KAZALD1 | NM_030929.5 | c.211A>T | p.Arg71Trp | missense_variant | 2/5 | ENST00000370200.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KAZALD1 | ENST00000370200.6 | c.211A>T | p.Arg71Trp | missense_variant | 2/5 | 1 | NM_030929.5 | P1 | |
KAZALD1 | ENST00000470106.1 | n.44-183A>T | intron_variant, non_coding_transcript_variant | 3 | |||||
KAZALD1 | ENST00000477979.5 | n.112+688A>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00913 AC: 1390AN: 152172Hom.: 19 Cov.: 33
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00211 AC: 433AN: 205554Hom.: 5 AF XY: 0.00157 AC XY: 181AN XY: 115278
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GnomAD4 exome AF: 0.000959 AC: 1367AN: 1425294Hom.: 33 Cov.: 33 AF XY: 0.000821 AC XY: 581AN XY: 707850
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GnomAD4 genome ? AF: 0.00921 AC: 1402AN: 152290Hom.: 20 Cov.: 33 AF XY: 0.00861 AC XY: 641AN XY: 74474
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3476
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 25, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
N
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Uncertain
D
Polyphen
B
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at