rs28720014

Variant names:

• chr4-118523301-G-A
• rs28720014
• ENST00000502249.6:n.3569G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000502249.6(CEP170P1):​n.3569G>A variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.449 in 1,569,808 control chromosomes in the GnomAD database, including 161,026 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 (16030 hom., cov: 27)
  • Exomes 𝑓: 0.45 (144996 hom.)
• Consequence: CEP170P1 ENST00000502249.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.79
• Publications: 4 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]

CEP170P1 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• 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.62-18G>A		intron_variant	Intron 1 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEP170P1	ENST00000502249.6	n.3569G>A		non_coding_transcript_exon_variant	Exon 11 of 17	6
CEP170P1	ENST00000755699.1	n.154G>A		non_coding_transcript_exon_variant	Exon 2 of 6
CEP170P1	ENST00000755694.1	n.114-18G>A		intron_variant	Intron 1 of 7

Frequencies

GnomAD3 genomes AF: 0.458 AC: 68642 AN: 149992 Hom.: 16013 Cov.: 27

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.636

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.589

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.463

GnomAD4 exome AF: 0.448 AC: 636483 AN: 1419692 Hom.: 144996 Cov.: 38 AF XY: 0.446 AC XY: 313054 AN XY: 702080

African (AFR) AF: 0.450 AC: 14656 AN: 32576

American (AMR) AF: 0.380 AC: 14382 AN: 37816

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 8675 AN: 25458

East Asian (EAS) AF: 0.622 AC: 23577 AN: 37896

South Asian (SAS) AF: 0.352 AC: 28369 AN: 80618

European-Finnish (FIN) AF: 0.578 AC: 29421 AN: 50936

Middle Eastern (MID) AF: 0.446 AC: 2555 AN: 5724

European-Non Finnish (NFE) AF: 0.448 AC: 488422 AN: 1089766

Other (OTH) AF: 0.449 AC: 26426 AN: 58902

GnomAD4 genome AF: 0.458 AC: 68707 AN: 150116 Hom.: 16030 Cov.: 27 AF XY: 0.461 AC XY: 33714 AN XY: 73152

African (AFR) AF: 0.452 AC: 18409 AN: 40716

American (AMR) AF: 0.396 AC: 5930 AN: 14976

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1188 AN: 3462

East Asian (EAS) AF: 0.634 AC: 3245 AN: 5122

South Asian (SAS) AF: 0.359 AC: 1679 AN: 4672

European-Finnish (FIN) AF: 0.589 AC: 5998 AN: 10192

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30579 AN: 67690

Other (OTH) AF: 0.466 AC: 972 AN: 2088

Alfa AF: 0.445 Hom.: 3114

Bravo AF: 0.449

Asia WGS AF: 0.499 AC: 1733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	20
DANN	Benign	0.86
PhyloP100		5.8

Splicing

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

Other links and lift over

dbSNP: rs28720014; hg19: chr4-119444456;