rs780818748

Variant names:

• chrX-134244820-A-G
• rs780818748
• NM_001353453.3:c.20A>G

Your query was ambiguous. Multiple possible variants found:

• chrX-134244820-A-G
• chrX-134244820-A-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001353453.3(CCDC160):​c.20A>G​(p.His7Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000684 in 1,168,995 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H7L) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.0000089 (0 hom., 1 hem., cov: 23)
  • Exomes 𝑓: 0.0000066 (0 hom. 0 hem.)
• Consequence: CCDC160 NM_001353453.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 2.47
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.22510299).

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.20A>G	p.His7Arg	missense	Exon 3 of 3	NP_001340382.1	A6NGH7
	CCDC160	NM_001101357.3		c.20A>G	p.His7Arg	missense	Exon 2 of 2	NP_001094827.1	A6NGH7
	CCDC160	NM_001393996.1		c.20A>G	p.His7Arg	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.20A>G	p.His7Arg	missense	Exon 3 of 3	ENSP00000511932.1	A6NGH7
	CCDC160	ENST00000370809.5	TSL:5	c.20A>G	p.His7Arg	missense	Exon 2 of 2	ENSP00000359845.4	A6NGH7
	CCDC160	ENST00000517294.5	TSL:5	c.20A>G	p.His7Arg	missense	Exon 3 of 3	ENSP00000427951.1	A6NGH7

Frequencies

GnomAD3 genomes AF: 0.00000891 AC: 1 AN: 112208 Hom.: 0 Cov.: 23

Gnomad AFR AF: 0.00

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: 0.0000188

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.0000152 AC: 2 AN: 131566 AF XY: 0.00

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: 0.00000662 AC: 7 AN: 1056787 Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0 AN XY: 338495

African (AFR) AF: 0.00 AC: 0 AN: 24597

American (AMR) AF: 0.00 AC: 0 AN: 25834

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17696

East Asian (EAS) AF: 0.00 AC: 0 AN: 29641

South Asian (SAS) AF: 0.0000641 AC: 3 AN: 46827

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 39362

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3985

European-Non Finnish (NFE) AF: 0.00000364 AC: 3 AN: 824479

Other (OTH) AF: 0.0000225 AC: 1 AN: 44366

GnomAD4 genome AF: 0.00000891 AC: 1 AN: 112208 Hom.: 0 Cov.: 23 AF XY: 0.0000291 AC XY: 1 AN XY: 34358

African (AFR) AF: 0.00 AC: 0 AN: 30893

American (AMR) AF: 0.00 AC: 0 AN: 10510

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2647

East Asian (EAS) AF: 0.00 AC: 0 AN: 3598

South Asian (SAS) AF: 0.00 AC: 0 AN: 2713

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6155

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 237

European-Non Finnish (NFE) AF: 0.0000188 AC: 1 AN: 53256

Other (OTH) AF: 0.00 AC: 0 AN: 1513

Alfa AF: 0.00 Hom.: 0

ExAC AF: 0.00000834 AC: 1

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	0.17
BayesDel_addAF	Benign	-0.13	T
BayesDel_noAF	Benign	-0.16
CADD	Benign	15
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.58	D
FATHMM_MKL	Uncertain	0.92	D
LIST_S2	Benign	0.44	T
M_CAP	Benign	0.0081	T
MetaRNN	Benign	0.23	T
MetaSVM	Benign	-0.80	T
MutationAssessor	Uncertain	2.3	M
PhyloP100		2.5
PrimateAI	Benign	0.47	T
PROVEAN	Pathogenic	-4.8	D
REVEL	Benign	0.15
Sift	Uncertain	0.021	D
Sift4G	Uncertain	0.043	D
Polyphen		0.98	D
Vest4		0.14
MutPred		0.28		Gain of MoRF binding (P = 0.0258)
MVP		0.33
MPC		0.0028
ClinPred		0.47	T
GERP RS		5.0
Varity_R		0.61
gMVP		0.079
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: rs780818748; hg19: chrX-133378850;