17-16708812-C-G

Variant names:

• chr17-16708812-C-G
• rs765491212
• NM_001382000.1:c.755C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001382000.1(CCDC144A):​c.755C>G​(p.Pro252Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,459,506 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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. P252Q) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: CCDC144A NM_001382000.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820
• Publications: 0 publications found

Genes affected

CCDC144A (HGNC:29072): (coiled-coil domain containing 144A)

ENSG00000266302 (HGNC:):

ACMG classification

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=0.050494254).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001382000.1. 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
	CCDC144A	NM_001382000.1	MANE Select	c.755C>G	p.Pro252Arg	missense	Exon 5 of 17	NP_001368929.1	C9JT67
	CCDC144A	NM_014695.3		c.755C>G	p.Pro252Arg	missense	Exon 5 of 18	NP_055510.1	A2RUR9-1
	CCDC144A	NR_130142.2		n.915C>G		non_coding_transcript_exon	Exon 5 of 16

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC144A	ENST00000399273.5	TSL:1 MANE Select	c.755C>G	p.Pro252Arg	missense	Exon 5 of 17	ENSP00000382215.1	C9JT67
	CCDC144A	ENST00000360524.12	TSL:1	c.755C>G	p.Pro252Arg	missense	Exon 5 of 18	ENSP00000353717.8	A2RUR9-1
	CCDC144A	ENST00000360495.9	TSL:1	n.755C>G		non_coding_transcript_exon	Exon 5 of 16	ENSP00000353685.5	A6NG92

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 6.85e-7 AC: 1 AN: 1459506 Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1 AN XY: 726068

African (AFR) AF: 0.00 AC: 0 AN: 33396

American (AMR) AF: 0.0000224 AC: 1 AN: 44716

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26120

East Asian (EAS) AF: 0.00 AC: 0 AN: 39666

South Asian (SAS) AF: 0.00 AC: 0 AN: 86122

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53416

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4136

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1111738

Other (OTH) AF: 0.00 AC: 0 AN: 60196

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.18	T
BayesDel_noAF	Benign	-0.50
CADD	Benign	8.0
DANN	Benign	0.62
DEOGEN2	Benign	0.0073	T
Eigen	Benign	-1.5
Eigen_PC	Benign	-1.6
FATHMM_MKL	Benign	0.015	N
LIST_S2	Benign	0.54	T
M_CAP	Benign	0.0025	T
MetaRNN	Benign	0.050	T
MetaSVM	Benign	-1.0	T
PhyloP100		0.082
PrimateAI	Uncertain	0.77	T
PROVEAN	Uncertain	-3.2	D
REVEL	Benign	0.062
Sift	Uncertain	0.015	D
Sift4G	Uncertain	0.017	D
Polyphen		0.12	B
Vest4		0.13
MutPred		0.24		Gain of solvent accessibility (P = 0.0789)
MVP		0.072
ClinPred		0.081	T
GERP RS		-0.15
Varity_R		0.073
gMVP		0.014

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: rs765491212; hg19: chr17-16612126;