rs10783231

Variant names:

• chr12-48184542-A-C
• rs10783231
• NM_001013635.4:c.420A>C

Your query was ambiguous. Multiple possible variants found:

• chr12-48184542-A-C
• chr12-48184542-A-G
• chr12-48184542-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001013635.4(CCDC184):​c.420A>C​(p.Glu140Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 1,553,894 control chromosomes in the GnomAD database, including 429,862 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.70 (37679 hom., cov: 29)
  • Exomes 𝑓: 0.74 (392183 hom.)
• Consequence: CCDC184 NM_001013635.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 23 publications found

Genes affected

CCDC184 (HGNC:33749): (coiled-coil domain containing 184) Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=8.957121E-7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001013635.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC184	NM_001013635.4	MANE Select	c.420A>C	p.Glu140Asp	missense	Exon 1 of 1	NP_001013657.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC184	ENST00000316554.5	TSL:6 MANE Select	c.420A>C	p.Glu140Asp	missense	Exon 1 of 1	ENSP00000320849.3

Frequencies

GnomAD3 genomes AF: 0.698 AC: 105940 AN: 151700 Hom.: 37649 Cov.: 29

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.811

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.722

GnomAD2 exomes AF: 0.669 AC: 105186 AN: 157124 AF XY: 0.681

Gnomad AFR exome AF: 0.645

Gnomad AMR exome AF: 0.469

Gnomad ASJ exome AF: 0.800

Gnomad EAS exome AF: 0.415

Gnomad FIN exome AF: 0.701

Gnomad NFE exome AF: 0.772

Gnomad OTH exome AF: 0.718

GnomAD4 exome AF: 0.743 AC: 1041905 AN: 1402076 Hom.: 392183 Cov.: 74 AF XY: 0.743 AC XY: 514812 AN XY: 693110

African (AFR) AF: 0.643 AC: 20756 AN: 32284

American (AMR) AF: 0.486 AC: 17779 AN: 36608

Ashkenazi Jewish (ASJ) AF: 0.801 AC: 20233 AN: 25248

East Asian (EAS) AF: 0.415 AC: 15322 AN: 36924

South Asian (SAS) AF: 0.676 AC: 54464 AN: 80594

European-Finnish (FIN) AF: 0.709 AC: 28546 AN: 40264

Middle Eastern (MID) AF: 0.826 AC: 4701 AN: 5690

European-Non Finnish (NFE) AF: 0.771 AC: 837665 AN: 1085992

Other (OTH) AF: 0.726 AC: 42439 AN: 58472

GnomAD4 genome AF: 0.698 AC: 106015 AN: 151818 Hom.: 37679 Cov.: 29 AF XY: 0.692 AC XY: 51309 AN XY: 74156

African (AFR) AF: 0.643 AC: 26624 AN: 41410

American (AMR) AF: 0.595 AC: 9084 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.811 AC: 2813 AN: 3468

East Asian (EAS) AF: 0.407 AC: 2068 AN: 5086

South Asian (SAS) AF: 0.653 AC: 3139 AN: 4806

European-Finnish (FIN) AF: 0.715 AC: 7541 AN: 10554

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.770 AC: 52275 AN: 67914

Other (OTH) AF: 0.717 AC: 1510 AN: 2106

Alfa AF: 0.743 Hom.: 94783

Bravo AF: 0.686

TwinsUK AF: 0.770 AC: 2854

ALSPAC AF: 0.761 AC: 2931

ESP6500AA AF: 0.668 AC: 2887

ESP6500EA AF: 0.785 AC: 6639

ExAC AF: 0.626 AC: 68884

Asia WGS AF: 0.537 AC: 1871 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.052
BayesDel_addAF	Benign	-0.81	T
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.3
DANN	Benign	0.54
DEOGEN2	Benign	0.0023	T
Eigen	Benign	-1.6
Eigen_PC	Benign	-1.6
FATHMM_MKL	Benign	0.0037	N
LIST_S2	Benign	0.17	T
MetaRNN	Benign	9.0e-7	T
MetaSVM	Benign	-0.96	T
MutationAssessor	Benign	-0.34	N
PhyloP100		-1.1
PROVEAN	Benign	0.80	N
REVEL	Benign	0.032
Sift	Benign	1.0	T
Sift4G	Benign	0.56	T
Polyphen		0.0	B
Vest4		0.033
MutPred		0.084		Loss of helix (P = 0.0444)
MPC		0.34
ClinPred		0.0012	T
GERP RS		-1.7
Varity_R		0.049
gMVP		0.024
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs10783231; hg19: chr12-48578325; COSMIC: COSV57251551; COSMIC: COSV57251551;