14-102348704-GC-AT

Variant names:

• chr14-102348704-GC-AT
• NM_032630.3:c.491_492delGCinsAT
• CINP p.Arg164His

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_032630.3(CINP):​c.491_492delGCinsAT​(p.Arg164His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. 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 Benign in ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CINP NM_032630.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.52
• Publications: 0 publications found

Genes affected

CINP (HGNC:23789): (cyclin dependent kinase 2 interacting protein) The protein encoded by this gene is reported to be a component of the DNA replication complex as well as a genome-maintenance protein. It may interact with proteins important for replication initiation and has been shown to bind chromatin at the G1 phase of the cell cycle and dissociate from chromatin with replication initiation. It may also serve to regulate checkpoint signaling as part of the DNA damage response. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032630.3. 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
	CINP	NM_032630.3	MANE Select	c.491_492delGCinsAT	p.Arg164His	missense	N/A	NP_116019.1	Q9BW66-1
	CINP	NM_001320046.2		c.*4_*5delGCinsAT		3_prime_UTR	Exon 4 of 4	NP_001306975.1	Q9BW66-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CINP	ENST00000216756.11	TSL:1 MANE Select	c.491_492delGCinsAT	p.Arg164His	missense	N/A	ENSP00000216756.6	Q9BW66-1
	CINP	ENST00000559504.5	TSL:1	n.491_492delGCinsAT		non_coding_transcript_exon	Exon 4 of 6	ENSP00000453846.1	H0YN33
	CINP	ENST00000536961.6	TSL:3	c.536_537delGCinsAT	p.Arg179His	missense	N/A	ENSP00000442057.2	Q9BW66-3

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr14-102815041;