ENST00000502249.6:n.1372-5845C>T

Variant names:

• chr4-118500958-C-T
• rs4833582
• ENST00000502249.6:n.1372-5845C>T

Variant summary

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

The ENST00000502249.6(CEP170P1):​n.1372-5845C>T variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.341
• Publications: 2 publications found

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]

ENSG00000296144 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000502249.6. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEP170P1	ENST00000502249.6	TSL:6	n.1372-5845C>T		intron	N/A
	ENSG00000296144	ENST00000736728.1		n.86-1079G>A		intron	N/A
	ENSG00000296144	ENST00000736729.1		n.56-1079G>A		intron	N/A

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

African (AFR) AF: 0.477 AC: 19020 AN: 39844

American (AMR) AF: 0.404 AC: 5979 AN: 14814

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1187 AN: 3462

East Asian (EAS) AF: 0.661 AC: 3262 AN: 4932

South Asian (SAS) AF: 0.378 AC: 1784 AN: 4716

European-Finnish (FIN) AF: 0.559 AC: 5060 AN: 9050

Middle Eastern (MID) AF: 0.440 AC: 124 AN: 282

European-Non Finnish (NFE) AF: 0.450 AC: 30335 AN: 67464

Other (OTH) AF: 0.471 AC: 960 AN: 2038

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.0
DANN	Benign	0.31
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs4833582; hg19: chr4-119422113;