4-118500958-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000502249.6(CEP170P1):n.1372-5845C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 147,492 control chromosomes in the GnomAD database, including 16,127 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 0.46 (16127 hom., cov: 27)
• Consequence: CEP170P1 ENST00000502249.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.341

Genes affected

CEP170P1 (HGNC:28364): (centrosomal protein 170 pseudogene 1) This locus appears to be a transcribed pseudogene similar to centrosomal protein 170kDa (CEP170). An approximately 50 kb region upstream of this locus also is homologous to CEP170, but is not transcribed. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP170P1	ENST00000502249.6	n.1372-5845C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.463 AC: 68227 AN: 147432 Hom.: 16112 Cov.: 27

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.663

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.429

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.463 AC: 68275 AN: 147492 Hom.: 16127 Cov.: 27 AF XY: 0.466 AC XY: 33332 AN XY: 71576

Gnomad4 AFR AF: 0.477

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.661

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.559

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.471

Alfa AF: 0.451 Hom.: 1896

Bravo AF: 0.459

Asia WGS AF: 0.511 AC: 1767 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	5.0
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4833582; hg19: chr4-119422113;