3-62330719-T-G

Variant names:

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

Variant summary

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

The NM_001291941.3(CEP15):​c.178-606T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0906 in 152,150 control chromosomes in the GnomAD database, including 773 homozygotes. 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: 𝑓 0.091 (773 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEP15	NM_001291941.3	c.178-606T>G		intron_variant	Intron 4 of 5	ENST00000462069.6	NP_001278870.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEP15	ENST00000462069.6	c.178-606T>G		intron_variant	Intron 4 of 5	1	NM_001291941.3	ENSP00000419977.1

Frequencies

GnomAD3 genomes AF: 0.0906 AC: 13774 AN: 152032 Hom.: 770 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.0882

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.0674

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0669

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.0906 AC: 13782 AN: 152150 Hom.: 773 Cov.: 32 AF XY: 0.0916 AC XY: 6816 AN XY: 74376

African (AFR) AF: 0.103 AC: 4278 AN: 41534

American (AMR) AF: 0.0881 AC: 1345 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 501 AN: 3466

East Asian (EAS) AF: 0.277 AC: 1431 AN: 5162

South Asian (SAS) AF: 0.132 AC: 636 AN: 4824

European-Finnish (FIN) AF: 0.0674 AC: 714 AN: 10586

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0669 AC: 4547 AN: 67996

Other (OTH) AF: 0.109 AC: 229 AN: 2108

Alfa AF: 0.0726 Hom.: 600

Bravo AF: 0.0925

Asia WGS AF: 0.190 AC: 657 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.3
DANN	Benign	0.68
PhyloP100		-0.071
Mutation Taster		=100/0	polymorphism (auto)

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;