X-134245102-C-A

Variant names:

• chrX-134245102-C-A
• NM_001353453.3:c.302C>A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_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
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.135

Genes affected

CCDC160 (HGNC:37286): (coiled-coil domain containing 160)

ACMG classification

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
CCDC160	NM_001353453.3	c.302C>A	p.Ser101Tyr	missense_variant	Exon 3 of 3	ENST00000695460.1	NP_001340382.1
CCDC160	NM_001101357.3	c.302C>A	p.Ser101Tyr	missense_variant	Exon 2 of 2		NP_001094827.1
CCDC160	NM_001393996.1	c.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
CCDC160	ENST00000695460.1	c.302C>A	p.Ser101Tyr	missense_variant	Exon 3 of 3		NM_001353453.3	ENSP00000511932.1
CCDC160	ENST00000370809.5	c.302C>A	p.Ser101Tyr	missense_variant	Exon 2 of 2	5		ENSP00000359845.4
CCDC160	ENST00000517294.5	c.302C>A	p.Ser101Tyr	missense_variant	Exon 3 of 3	5		ENSP00000427951.1

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

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;