rs11581

chr9-97376879-A-Cchr9-97376879-A-G

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_020893.6(CCDC180):c.4959A>C(p.Gln1653His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CCDC180 NM_020893.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.888

Genes affected

CCDC180 (HGNC:29303): (coiled-coil domain containing 180) The protein encoded by this gene contains a coiled-coil domain. Alternative splicing results in multiple transcript variants encoding different isoforms. A single nucleotide polymorphism (SNP) in this gene has been associated with increased susceptibility to Behcet's Disease (PMID: 19442274). [provided by RefSeq, Dec 2016]

SUGT1P4-STRA6LP-CCDC180 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC180	NM_020893.6	c.4959A>C	p.Gln1653His	missense_variant	37/37	ENST00000529487.3
SUGT1P4-STRA6LP-CCDC180	NR_036528.1	n.6514A>C		non_coding_transcript_exon_variant	51/51
SUGT1P4-STRA6LP-CCDC180	NR_036527.1	n.5932A>C		non_coding_transcript_exon_variant	49/49
SUGT1P4-STRA6LP-CCDC180	NR_036529.1	n.5381A>C		non_coding_transcript_exon_variant	45/45

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC180	ENST00000529487.3	c.4959A>C	p.Gln1653His	missense_variant	37/37	1	NM_020893.6	P1
CCDC180	ENST00000487976.2	n.3030A>C		non_coding_transcript_exon_variant	3/3	1
CCDC180	ENST00000526038.1	n.6239A>C		non_coding_transcript_exon_variant	3/3	5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.19
BayesDel_addAF	Benign	-0.21	T
BayesDel_noAF	Benign	-0.54
Cadd	Benign	15
Dann	Uncertain	1.0
Eigen	Benign	-0.20
Eigen_PC	Benign	-0.38
FATHMM_MKL	Benign	0.085	N
LIST_S2	Benign	0.48	T
M_CAP	Benign	0.0067	T
MetaRNN	Uncertain	0.48	T
MetaSVM	Benign	-1.0	T
MutationTaster	Benign	0.96	P;P;P;P
PrimateAI	Benign	0.25	T
PROVEAN	Uncertain	-3.0	D
REVEL	Benign	0.081
Sift	Uncertain	0.012	D
Sift4G	Pathogenic	0.0010	D
Vest4		0.18
MVP		0.28
ClinPred		0.66	D
GERP RS		2.1
Varity_R		0.11
gMVP		0.067

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

LitVar

Other links and lift over

dbSNP: rs11581; hg19: chr9-100139161;