5-132998782-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001300816.3(ZCCHC10):​c.380G>A​(p.Ser127Asn) variant causes a missense change. The variant allele was found at a frequency of 0.00053 in 1,614,166 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00039 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00054 ( 0 hom. )

Consequence

ZCCHC10
NM_001300816.3 missense

Scores

3
6
10

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 6.55
Variant links:
Genes affected
ZCCHC10 (HGNC:25954): (zinc finger CCHC-type containing 10) Predicted to enable nucleic acid binding activity and zinc ion binding activity. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.05691755).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ZCCHC10NM_001300816.3 linkc.380G>A p.Ser127Asn missense_variant 5/5 ENST00000509437.6 NP_001287745.1 Q8TBK6-1B4DU89

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ZCCHC10ENST00000509437.6 linkc.380G>A p.Ser127Asn missense_variant 5/51 NM_001300816.3 ENSP00000423276.1 Q8TBK6-1

Frequencies

GnomAD3 genomes
AF:
0.000388
AC:
59
AN:
152182
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000483
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000655
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000823
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000247
AC:
62
AN:
251420
Hom.:
0
AF XY:
0.000272
AC XY:
37
AN XY:
135900
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000578
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.0000924
Gnomad NFE exome
AF:
0.000510
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000545
AC:
796
AN:
1461866
Hom.:
0
Cov.:
32
AF XY:
0.000472
AC XY:
343
AN XY:
727236
show subpopulations
Gnomad4 AFR exome
AF:
0.0000299
Gnomad4 AMR exome
AF:
0.0000671
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.0000936
Gnomad4 NFE exome
AF:
0.000682
Gnomad4 OTH exome
AF:
0.000480
GnomAD4 genome
AF:
0.000387
AC:
59
AN:
152300
Hom.:
0
Cov.:
32
AF XY:
0.000295
AC XY:
22
AN XY:
74472
show subpopulations
Gnomad4 AFR
AF:
0.0000481
Gnomad4 AMR
AF:
0.0000654
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000823
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000469
Hom.:
0
Bravo
AF:
0.000393
TwinsUK
AF:
0.00
AC:
0
ALSPAC
AF:
0.00156
AC:
6
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000698
AC:
6
ExAC
AF:
0.000214
AC:
26
Asia WGS
AF:
0.000289
AC:
1
AN:
3478
EpiCase
AF:
0.000709
EpiControl
AF:
0.000593

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsApr 01, 2024The c.314G>A (p.S105N) alteration is located in exon 4 (coding exon 4) of the ZCCHC10 gene. This alteration results from a G to A substitution at nucleotide position 314, causing the serine (S) at amino acid position 105 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.14
BayesDel_addAF
Benign
-0.35
T
BayesDel_noAF
Benign
-0.29
CADD
Uncertain
24
DANN
Uncertain
0.98
DEOGEN2
Benign
0.11
.;T;T;T
Eigen
Pathogenic
0.69
Eigen_PC
Pathogenic
0.67
FATHMM_MKL
Uncertain
0.97
D
LIST_S2
Benign
0.74
T;T;T;T
M_CAP
Benign
0.028
D
MetaRNN
Benign
0.057
T;T;T;T
MetaSVM
Uncertain
-0.051
T
MutationAssessor
Uncertain
2.2
.;.;M;.
PrimateAI
Uncertain
0.57
T
PROVEAN
Benign
-1.8
N;N;N;N
REVEL
Benign
0.16
Sift
Pathogenic
0.0
D;D;D;D
Sift4G
Uncertain
0.0060
D;D;D;D
Polyphen
0.99
D;.;D;D
Vest4
0.38
MVP
0.030
MPC
0.17
ClinPred
0.13
T
GERP RS
4.8
Varity_R
0.34
gMVP
0.28

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: rs144120476; hg19: chr5-132334474; API