rs12358699

Variant names:

• chr10-45058281-G-A
• rs12358699
• ENST00000456938.6:n.411+7246C>T

Variant summary

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

The ENST00000456938.6(CEP164P1):​n.411+7246C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0422 in 152,328 control chromosomes in the GnomAD database, including 140 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 0.042 (140 hom., cov: 33)
• Consequence: CEP164P1 ENST00000456938.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

Genes affected

CEP164P1 (HGNC:44988): (centrosomal protein 164 pseudogene 1)

ENSG00000277757 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEP164P1	ENST00000456938.6	n.411+7246C>T		intron_variant	Intron 5 of 6	1
CEP164P1	ENST00000598522.5	n.764+7246C>T		intron_variant	Intron 4 of 4	5
ENSG00000277757	ENST00000599308.3	n.765-42113C>T		intron_variant	Intron 7 of 7	5

Frequencies

GnomAD3 genomes AF: 0.0423 AC: 6438 AN: 152210 Hom.: 140 Cov.: 33

Gnomad AFR AF: 0.0324

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0264

Gnomad ASJ AF: 0.0357

Gnomad EAS AF: 0.0806

Gnomad SAS AF: 0.0282

Gnomad FIN AF: 0.0441

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0509

Gnomad OTH AF: 0.0349

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

GnomAD4 genome AF: 0.0422 AC: 6435 AN: 152328 Hom.: 140 Cov.: 33 AF XY: 0.0417 AC XY: 3108 AN XY: 74476

Gnomad4 AFR AF: 0.0324

Gnomad4 AMR AF: 0.0263

Gnomad4 ASJ AF: 0.0357

Gnomad4 EAS AF: 0.0806

Gnomad4 SAS AF: 0.0282

Gnomad4 FIN AF: 0.0441

Gnomad4 NFE AF: 0.0509

Gnomad4 OTH AF: 0.0346

Alfa AF: 0.0442 Hom.: 142

Bravo AF: 0.0396

Asia WGS AF: 0.0610 AC: 213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	1.4
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12358699; hg19: chr10-45553729;