rs200713204

Variant names:

• chr19-47260651-G-A
• rs200713204
• NM_015603.3:c.274G>A

Your query was ambiguous. Multiple possible variants found:

• chr19-47260651-G-A
• chr19-47260651-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_015603.3(CCDC9):​c.274G>A​(p.Gly92Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000364 in 1,372,398 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 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 nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000036 (0 hom.)
• Consequence: CCDC9 NM_015603.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.91

Genes affected

CCDC9 (HGNC:24560): (coiled-coil domain containing 9) Enables RNA binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.16332516).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC9	NM_015603.3	c.274G>A	p.Gly92Arg	missense_variant	Exon 5 of 12	ENST00000221922.11	NP_056418.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC9	ENST00000221922.11	c.274G>A	p.Gly92Arg	missense_variant	Exon 5 of 12	1	NM_015603.3	ENSP00000221922.5
CCDC9	ENST00000643617.1	c.274G>A	p.Gly92Arg	missense_variant	Exon 5 of 14			ENSP00000494410.1
CCDC9	ENST00000599398.5	c.274G>A	p.Gly92Arg	missense_variant	Exon 5 of 5	3		ENSP00000469717.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD3 exomes AF: 0.00000602 AC: 1 AN: 166232 Hom.: 0 AF XY: 0.0000111 AC XY: 1 AN XY: 89790

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000660

Gnomad SAS 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: 0.00000364 AC: 5 AN: 1372398 Hom.: 0 Cov.: 32 AF XY: 0.00000592 AC XY: 4 AN XY: 675904

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000256

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000371

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.21
BayesDel_addAF	Benign	-0.25	T
BayesDel_noAF	Benign	-0.41
CADD	Uncertain	24
DANN	Uncertain	0.99
DEOGEN2	Benign	0.0057	T;.;.
Eigen	Benign	0.15
Eigen_PC	Benign	0.016
FATHMM_MKL	Benign	0.71	D
LIST_S2	Uncertain	0.86	D;D;D
M_CAP	Benign	0.026	D
MetaRNN	Benign	0.16	T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.84	L;.;.
PrimateAI	Uncertain	0.56	T
PROVEAN	Benign	-0.38	N;.;.
REVEL	Benign	0.16
Sift	Uncertain	0.021	D;.;.
Sift4G	Benign	0.35	T;.;T
Polyphen		1.0	D;.;.
Vest4		0.40
MutPred		0.17		Gain of solvent accessibility (P = 0.0037);Gain of solvent accessibility (P = 0.0037);Gain of solvent accessibility (P = 0.0037);
MVP		0.44
MPC		0.18
ClinPred		0.38	T
GERP RS		2.3
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.040
gMVP		0.31

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: rs200713204; hg19: chr19-47763908;