Genetic Variant CCDC160:p.Ile316Ile (chrX-134245748-C-T) – ACMG Classification: Benign (-9 pts)

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_StrongBP7BS2

The NM_001353453.3(CCDC160):c.948C>T(p.Ile316Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000612 in 1,143,927 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000027 ( 0 hom., 0 hem., cov: 23)

Exomes 𝑓: 0.0000039 ( 0 hom. 2 hem. )

Consequence

CCDC160
NM_001353453.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.367

Publications

0 publications found

Variant links:

Genes affected

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

CCDC160 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP7

Synonymous conserved (PhyloP=-0.367 with no splicing effect.

BS2

High Hemizygotes in GnomAdExome4 at 2 gene

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.948C>T	p.Ile316Ile	synonymous	Exon 3 of 3	NP_001340382.1	A6NGH7
CCDC160	NM_001101357.3		c.948C>T	p.Ile316Ile	synonymous	Exon 2 of 2	NP_001094827.1	A6NGH7
CCDC160	NM_001393996.1		c.948C>T	p.Ile316Ile	synonymous	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.948C>T	p.Ile316Ile	synonymous	Exon 3 of 3	ENSP00000511932.1	A6NGH7
CCDC160	ENST00000370809.5	TSL:5	c.948C>T	p.Ile316Ile	synonymous	Exon 2 of 2	ENSP00000359845.4	A6NGH7
CCDC160	ENST00000517294.5	TSL:5	c.948C>T	p.Ile316Ile	synonymous	Exon 3 of 3	ENSP00000427951.1	A6NGH7

Frequencies

GnomAD3 genomes

AF:

0.0000270

AC:

AN:

111278

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000981

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

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:

0.00

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000178

AC:

AN:

112658

AF XY:

0.0000379

show subpopulations

Gnomad AFR exome

AF:

0.000225

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:

0.00000387

AC:

AN:

1032649

Hom.:

Cov.:

AF XY:

0.00000623

AC XY:

AN XY:

321089

show subpopulations

African (AFR)

AF:

0.000169

AC:

AN:

23620

American (AMR)

AF:

0.00

AC:

AN:

21863

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

17030

East Asian (EAS)

AF:

0.00

AC:

AN:

28621

South Asian (SAS)

AF:

0.00

AC:

AN:

42902

European-Finnish (FIN)

AF:

0.00

AC:

AN:

38474

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3924

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

812888

Other (OTH)

AF:

0.00

AC:

AN:

43327

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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

AF:

0.0000270

AC:

AN:

111278

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

33472

show subpopulations

African (AFR)

AF:

0.0000981

AC:

AN:

30582

American (AMR)

AF:

0.00

AC:

AN:

10476

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2639

East Asian (EAS)

AF:

0.00

AC:

AN:

3569

South Asian (SAS)

AF:

0.00

AC:

AN:

2623

European-Finnish (FIN)

AF:

0.00

AC:

AN:

5943

Middle Eastern (MID)

AF:

0.00

AC:

AN:

235

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

53023

Other (OTH)

AF:

0.00

AC:

AN:

1504

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome 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

Alfa

AF:

0.0000712

Hom.:

Bravo

AF:

0.0000302

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

0.74

(source)

DANN

Benign

0.41

PhyloP100

-0.37

Mutation Taster

=100/0

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over