chr10-45008431-C-T

Variant names:

• chr10-45008431-C-T
• rs2210497
• ENST00000456938.6:n.619-4356G>A

Variant summary

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

The ENST00000456938.6(CEP164P1):​n.619-4356G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 152,076 control chromosomes in the GnomAD database, including 20,367 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 0.49 (20367 hom., cov: 33)
• Consequence: CEP164P1 ENST00000456938.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.509

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.612 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.619-4356G>A		intron_variant	Intron 6 of 6	1

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74125 AN: 151958 Hom.: 20365 Cov.: 33

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.487 AC: 74130 AN: 152076 Hom.: 20367 Cov.: 33 AF XY: 0.491 AC XY: 36499 AN XY: 74344

Gnomad4 AFR AF: 0.242

Gnomad4 AMR AF: 0.537

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.659

Gnomad4 NFE AF: 0.617

Gnomad4 OTH AF: 0.506

Alfa AF: 0.410 Hom.: 1274

Bravo AF: 0.467

Asia WGS AF: 0.382 AC: 1330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.2
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2210497; hg19: chr10-45503879;