rs10018120

Variant names:

• chr4-118521846-A-G
• rs10018120
• ENST00000502249.6:n.3479-1365A>G

Variant summary

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

The NR_003135.3(CEP170P1):​n.62-1473A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 151,940 control chromosomes in the GnomAD database, including 16,194 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 (16194 hom., cov: 32)
• Consequence: CEP170P1 NR_003135.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEP170P1	NR_003135.3	n.62-1473A>G		intron_variant	Intron 1 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEP170P1	ENST00000502249.6	n.3479-1365A>G		intron_variant	Intron 10 of 16	6

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69370 AN: 151824 Hom.: 16178 Cov.: 32

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.457 AC: 69433 AN: 151940 Hom.: 16194 Cov.: 32 AF XY: 0.460 AC XY: 34157 AN XY: 74222

Gnomad4 AFR AF: 0.451

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.634

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.588

Gnomad4 NFE AF: 0.451

Gnomad4 OTH AF: 0.462

Alfa AF: 0.460 Hom.: 2083

Bravo AF: 0.448

Asia WGS AF: 0.499 AC: 1734 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.9
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10018120; hg19: chr4-119443001;