Genetic Variant CCDC160:p.Ser101Cys (chrX-134245102-C-G) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001353453.3(CCDC160):c.302C>G(p.Ser101Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,074,628 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S101Y) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 23)

Exomes 𝑓: 0.0000019 ( 0 hom. 0 hem. )

Consequence

CCDC160
NM_001353453.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.135

Publications

0 publications found

Variant links:

Genes affected

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

CCDC160 links:

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ACMG classification

Classification was made for transcript

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=0.063970655).

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

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
CCDC160	NM_001353453.3	MANE Select	c.302C>G	p.Ser101Cys	missense	Exon 3 of 3	NP_001340382.1	A6NGH7
CCDC160	NM_001101357.3		c.302C>G	p.Ser101Cys	missense	Exon 2 of 2	NP_001094827.1	A6NGH7
CCDC160	NM_001393996.1		c.302C>G	p.Ser101Cys	missense	Exon 3 of 3	NP_001380925.1	A6NGH7

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
CCDC160	ENST00000695460.1	MANE Select	c.302C>G	p.Ser101Cys	missense	Exon 3 of 3	ENSP00000511932.1	A6NGH7
CCDC160	ENST00000370809.5	TSL:5	c.302C>G	p.Ser101Cys	missense	Exon 2 of 2	ENSP00000359845.4	A6NGH7
CCDC160	ENST00000517294.5	TSL:5	c.302C>G	p.Ser101Cys	missense	Exon 3 of 3	ENSP00000427951.1	A6NGH7

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.00000690

AC:

AN:

145021

AF XY:

0.00

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000186

AC:

AN:

1074628

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

347730

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

25940

American (AMR)

AF:

0.00

AC:

AN:

32012

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

18906

East Asian (EAS)

AF:

0.00

AC:

AN:

29531

South Asian (SAS)

AF:

0.0000394

AC:

AN:

50822

European-Finnish (FIN)

AF:

0.00

AC:

AN:

39467

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4108

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

828524

Other (OTH)

AF:

0.00

AC:

AN:

45318

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.450

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.084

BayesDel_addAF

Benign

-0.46

BayesDel_noAF

Benign

-0.89

CADD

Benign

6.7

(source)

DANN

Benign

0.95

DEOGEN2

Benign

0.28

FATHMM_MKL

Benign

0.029

LIST_S2

Benign

0.39

M_CAP

Benign

0.017

MetaRNN

Benign

0.064

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.9

PhyloP100

-0.14

PrimateAI

Benign

0.27

PROVEAN

Uncertain

-2.5

REVEL

Benign

0.016

Sift

Benign

0.19

Sift4G

Benign

0.083

Polyphen

0.020

Vest4

0.16

MutPred

0.20

Loss of relative solvent accessibility (P = 0.0071)

MVP

0.014

MPC

0.0055

ClinPred

0.050

GERP RS

-1.2

Varity_R

0.087

gMVP

0.023

Mutation Taster

=95/5

polymorphism

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over