chrX-134245102-C-A

Variant names:

• chrX-134245102-C-A
• rs1475940065
• NM_001353453.3:c.302C>A

Variant summary

Our verdict is Likely benign. The variant received -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. 15/20 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
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.055134535).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001353453.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC160	NM_001353453.3	MANE Select	c.302C>A	p.Ser101Tyr	missense	Exon 3 of 3	NP_001340382.1	A6NGH7
	CCDC160	NM_001101357.3		c.302C>A	p.Ser101Tyr	missense	Exon 2 of 2	NP_001094827.1	A6NGH7
	CCDC160	NM_001393996.1		c.302C>A	p.Ser101Tyr	missense	Exon 3 of 3	NP_001380925.1	A6NGH7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC160	ENST00000695460.1	MANE Select	c.302C>A	p.Ser101Tyr	missense	Exon 3 of 3	ENSP00000511932.1	A6NGH7
	CCDC160	ENST00000370809.5	TSL:5	c.302C>A	p.Ser101Tyr	missense	Exon 2 of 2	ENSP00000359845.4	A6NGH7
	CCDC160	ENST00000517294.5	TSL:5	c.302C>A	p.Ser101Tyr	missense	Exon 3 of 3	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

African (AFR) AF: 0.00 AC: 0 AN: 25940

American (AMR) AF: 0.00 AC: 0 AN: 32012

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18906

East Asian (EAS) AF: 0.00 AC: 0 AN: 29531

South Asian (SAS) AF: 0.00 AC: 0 AN: 50822

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 39467

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4108

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 828523

Other (OTH) AF: 0.00 AC: 0 AN: 45318

GnomAD4 genome Cov.: 23

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

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
FATHMM_MKL	Benign	0.042	N
LIST_S2	Benign	0.41	T
M_CAP	Benign	0.011	T
MetaRNN	Benign	0.055	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.6	L
PhyloP100		-0.14
PrimateAI	Benign	0.29	T
PROVEAN	Benign	-2.0	N
REVEL	Benign	0.014
Sift	Benign	1.0	T
Sift4G	Benign	0.068	T
Polyphen		0.082	B
Vest4		0.11
MutPred		0.24		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
Mutation Taster		=95/5	polymorphism

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

Other links and lift over

dbSNP: rs1475940065; hg19: chrX-133379132;