3-62330719-T-A

Variant names:

• chr3-62330719-T-A
• rs3774700
• NM_001291941.3:c.178-606T>A

Variant summary

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

The NM_001291941.3(CEP15):​c.178-606T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 32)
• Consequence: CEP15 NM_001291941.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710
• Publications: 4 publications found

Genes affected

CEP15 (HGNC:25024): (centrosomal protein 15)

PTPRG-AS1 (HGNC:44638): (PTPRG antisense RNA 1)

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 (BayesDel_noAF=-0.82).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001291941.3. 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
	CEP15	NM_001291941.3	MANE Select	c.178-606T>A		intron	N/A	NP_001278870.1
	CEP15	NM_001291942.3		c.178-606T>A		intron	N/A	NP_001278871.1
	CEP15	NM_020685.6		c.178-606T>A		intron	N/A	NP_065736.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEP15	ENST00000462069.6	TSL:1 MANE Select	c.178-606T>A		intron	N/A	ENSP00000419977.1
	CEP15	ENST00000494481.5	TSL:1	c.178-606T>A		intron	N/A	ENSP00000418086.1
	CEP15	ENST00000542214.2	TSL:1	c.178-606T>A		intron	N/A	ENSP00000438275.1

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

Alfa AF: 0.00 Hom.: 600

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.2
DANN	Benign	0.58
PhyloP100		-0.071

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: rs3774700; hg19: chr3-62316394;