chrX-134245102-C-A

Variant summary

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

The NM_001353453.3(CCDC160):​c.302C>A​(p.Ser101Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 23)
Exomes 𝑓: 0.0 ( 0 hom. 0 hem. )
Failed GnomAD Quality Control

Consequence

CCDC160
NM_001353453.3 missense

Scores

1
16

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.135
Variant links:
Genes affected
CCDC160 (HGNC:37286): (coiled-coil domain containing 160)

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=0.055134535).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CCDC160NM_001353453.3 linkc.302C>A p.Ser101Tyr missense_variant Exon 3 of 3 ENST00000695460.1 NP_001340382.1
CCDC160NM_001101357.3 linkc.302C>A p.Ser101Tyr missense_variant Exon 2 of 2 NP_001094827.1 A6NGH7
CCDC160NM_001393996.1 linkc.302C>A p.Ser101Tyr missense_variant Exon 3 of 3 NP_001380925.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CCDC160ENST00000695460.1 linkc.302C>A p.Ser101Tyr missense_variant Exon 3 of 3 NM_001353453.3 ENSP00000511932.1 A6NGH7
CCDC160ENST00000370809.5 linkc.302C>A p.Ser101Tyr missense_variant Exon 2 of 2 5 ENSP00000359845.4 A6NGH7
CCDC160ENST00000517294.5 linkc.302C>A p.Ser101Tyr missense_variant Exon 3 of 3 5 ENSP00000427951.1 A6NGH7

Frequencies

GnomAD3 genomes
Cov.:
23
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1074627
Hom.:
0
Cov.:
29
AF XY:
0.00
AC XY:
0
AN XY:
347729
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
23

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Feb 06, 2023
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.302C>A (p.S101Y) alteration is located in exon 2 (coding exon 1) of the CCDC160 gene. This alteration results from a C to A substitution at nucleotide position 302, causing the serine (S) at amino acid position 101 to be replaced by a tyrosine (Y). 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
0.12
BayesDel_addAF
Benign
-0.47
T
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.074
DANN
Benign
0.27
DEOGEN2
Uncertain
0.42
T;T
FATHMM_MKL
Benign
0.042
N
LIST_S2
Benign
0.41
T;.
M_CAP
Benign
0.011
T
MetaRNN
Benign
0.055
T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.6
L;L
PrimateAI
Benign
0.29
T
PROVEAN
Benign
-2.0
N;N
REVEL
Benign
0.014
Sift
Benign
1.0
T;T
Sift4G
Benign
0.068
T;T
Polyphen
0.082
B;B
Vest4
0.11
MutPred
0.24
Loss of glycosylation at S101 (P = 0.0104);Loss of glycosylation at S101 (P = 0.0104);
MVP
0.014
MPC
0.0040
ClinPred
0.042
T
GERP RS
-1.2
Varity_R
0.044
gMVP
0.027

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

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-133379132; API