10-45021899-C-T

Variant names:

• chr10-45021899-C-T
• rs2018728
• ENST00000456938.6:n.412-5731G>A

Variant summary

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

The ENST00000456938.6(CEP164P1):​n.412-5731G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 152,000 control chromosomes in the GnomAD database, including 23,318 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 0.53 (23318 hom., cov: 32)
• Consequence: CEP164P1 ENST00000456938.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.455

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=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.653 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.412-5731G>A		intron_variant	Intron 5 of 6	1
CEP164P1	ENST00000598522.5	n.765-5731G>A		intron_variant	Intron 4 of 4	5
ENSG00000277757	ENST00000599308.3	n.765-5731G>A		intron_variant	Intron 7 of 7	5

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79939 AN: 151882 Hom.: 23312 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.505

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.525

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.526 AC: 79962 AN: 152000 Hom.: 23318 Cov.: 32 AF XY: 0.527 AC XY: 39168 AN XY: 74262

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.574

Gnomad4 ASJ AF: 0.585

Gnomad4 EAS AF: 0.199

Gnomad4 SAS AF: 0.524

Gnomad4 FIN AF: 0.682

Gnomad4 NFE AF: 0.658

Gnomad4 OTH AF: 0.560

Alfa AF: 0.600 Hom.: 13128

Bravo AF: 0.507

Asia WGS AF: 0.401 AC: 1397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2018728; hg19: chr10-45517347;