rs1866560618

Variant names:

• chr11-67507596-A-C
• rs1866560618
• NM_005851.5:c.176T>G

Your query was ambiguous. Multiple possible variants found:

• chr11-67507596-A-C
• chr11-67507596-A-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_005851.5(CDK2AP2):​c.176T>G​(p.Val59Gly) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,461,238 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: CDK2AP2 NM_005851.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.80

Genes affected

CDK2AP2 (HGNC:30833): (cyclin dependent kinase 2 associated protein 2) This gene encodes a protein that interacts with cyclin-dependent kinase 2 associated protein 1. Pseudogenes associated with this gene are located on chromosomes 7 and 9. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Dec 2012]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.32188314).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDK2AP2	NM_005851.5	c.176T>G	p.Val59Gly	missense_variant	Exon 2 of 4	ENST00000301488.8	NP_005842.1
CDK2AP2	NM_001271849.2	c.11T>G	p.Val4Gly	missense_variant	Exon 2 of 4		NP_001258778.1
CDK2AP2	NR_073484.2	n.567T>G		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDK2AP2	ENST00000301488.8	c.176T>G	p.Val59Gly	missense_variant	Exon 2 of 4	1	NM_005851.5	ENSP00000301488.4

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1461238 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 726920

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.0000331

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.59
BayesDel_addAF	Pathogenic	0.32	D
BayesDel_noAF	Pathogenic	0.22
CADD	Pathogenic	26
DANN	Uncertain	1.0
DEOGEN2	Benign	0.079	T;.
Eigen	Uncertain	0.40
Eigen_PC	Uncertain	0.45
FATHMM_MKL	Uncertain	0.93	D
LIST_S2	Benign	0.67	T;T
M_CAP	Benign	0.0090	T
MetaRNN	Benign	0.32	T;T
MetaSVM	Benign	-0.83	T
MutationAssessor	Benign	1.0	L;.
PrimateAI	Uncertain	0.68	T
PROVEAN	Benign	-0.91	N;N
REVEL	Uncertain	0.32
Sift	Uncertain	0.010	D;D
Sift4G	Benign	0.19	T;T
Polyphen		0.95	P;.
Vest4		0.49
MutPred		0.35		Loss of sheet (P = 0.0181);Loss of sheet (P = 0.0181);
MVP		0.57
MPC		2.5
ClinPred		0.90	D
GERP RS		5.3
Varity_R		0.30
gMVP		0.84

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: rs1866560618; hg19: chr11-67275067;