chrX-134244907-C-T

Variant names:

• chrX-134244907-C-T
• rs375551602
• NM_001353453.3:c.107C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The NM_001353453.3(CCDC160):​c.107C>T​(p.Thr36Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000599 in 1,202,818 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 21 hemizygotes in GnomAD. 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 Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.000045 (0 hom., 0 hem., cov: 23)
  • Exomes 𝑓: 0.000061 (0 hom. 21 hem.)
• Consequence: CCDC160 NM_001353453.3 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.274
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.02270183).
• BP6: Variant X-134244907-C-T is Benign according to our data. Variant chrX-134244907-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2592063.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Hemizygotes in GnomAdExome4 at 21 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC160	NM_001353453.3	MANE Select	c.107C>T	p.Thr36Met	missense	Exon 3 of 3	NP_001340382.1	A6NGH7
	CCDC160	NM_001101357.3		c.107C>T	p.Thr36Met	missense	Exon 2 of 2	NP_001094827.1	A6NGH7
	CCDC160	NM_001393996.1		c.107C>T	p.Thr36Met	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.107C>T	p.Thr36Met	missense	Exon 3 of 3	ENSP00000511932.1	A6NGH7
	CCDC160	ENST00000370809.5	TSL:5	c.107C>T	p.Thr36Met	missense	Exon 2 of 2	ENSP00000359845.4	A6NGH7
	CCDC160	ENST00000517294.5	TSL:5	c.107C>T	p.Thr36Met	missense	Exon 3 of 3	ENSP00000427951.1	A6NGH7

Frequencies

GnomAD3 genomes AF: 0.0000448 AC: 5 AN: 111579 Hom.: 0 Cov.: 23

Gnomad AFR AF: 0.0000652

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: 0.0000565

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.0000301 AC: 5 AN: 165894 AF XY: 0.0000185

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: 0.0000412

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000614 AC: 67 AN: 1091239 Hom.: 0 Cov.: 30 AF XY: 0.0000587 AC XY: 21 AN XY: 357753

African (AFR) AF: 0.00 AC: 0 AN: 26315

American (AMR) AF: 0.00 AC: 0 AN: 34494

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19245

East Asian (EAS) AF: 0.00 AC: 0 AN: 30085

South Asian (SAS) AF: 0.0000382 AC: 2 AN: 52386

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 40229

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4126

European-Non Finnish (NFE) AF: 0.0000775 AC: 65 AN: 838486

Other (OTH) AF: 0.00 AC: 0 AN: 45873

GnomAD4 genome AF: 0.0000448 AC: 5 AN: 111579 Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0 AN XY: 33831

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0000652 AC: 2 AN: 30689

American (AMR) AF: 0.00 AC: 0 AN: 10435

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2639

East Asian (EAS) AF: 0.00 AC: 0 AN: 3600

South Asian (SAS) AF: 0.00 AC: 0 AN: 2698

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 5978

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 236

European-Non Finnish (NFE) AF: 0.0000565 AC: 3 AN: 53125

Other (OTH) AF: 0.00 AC: 0 AN: 1496

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.00000000000315292), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.000142 Hom.: 1

Bravo AF: 0.0000491

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000314 AC: 2

ExAC AF: 0.0000332 AC: 4

ClinVar

ClinVar submissions

Significance: Likely benign

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	0.084
BayesDel_addAF	Benign	-0.53	T
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.075
DANN	Benign	0.11
DEOGEN2	Benign	0.057	T
FATHMM_MKL	Benign	0.0030	N
LIST_S2	Benign	0.42	T
M_CAP	Benign	0.0042	T
MetaRNN	Benign	0.023	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	-0.49	N
PhyloP100		-0.27
PrimateAI	Benign	0.22	T
PROVEAN	Benign	0.88	N
REVEL	Benign	0.032
Sift	Benign	0.39	T
Sift4G	Benign	0.17	T
Polyphen		0.029	B
Vest4		0.048
MVP		0.014
MPC		0.0056
ClinPred		0.028	T
GERP RS		-7.5
Varity_R		0.016
gMVP		0.026
Mutation Taster		=99/1	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: rs375551602; hg19: chrX-133378937;