10-45052620-A-G

Position:

• chr10-45052620-A-G

Variant summary

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

The variant allele was found at a frequency of 0.774 in 152,084 control chromosomes in the GnomAD database, including 45,700 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 0.77 (45700 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

Genes affected

CEP164P1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.45052620A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEP164P1	ENST00000456938.6	n.411+12907T>C		intron_variant		1
CEP164P1	ENST00000598522.5	n.764+12907T>C		intron_variant		5
ENSG00000277757	ENST00000599308.3	n.765-36452T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.774 AC: 117657 AN: 151966 Hom.: 45665 Cov.: 32

Gnomad AFR AF: 0.809

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.758

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

GnomAD4 genome AF: 0.774 AC: 117746 AN: 152084 Hom.: 45700 Cov.: 32 AF XY: 0.775 AC XY: 57590 AN XY: 74316

Gnomad4 AFR AF: 0.809

Gnomad4 AMR AF: 0.774

Gnomad4 ASJ AF: 0.675

Gnomad4 EAS AF: 0.591

Gnomad4 SAS AF: 0.750

Gnomad4 FIN AF: 0.790

Gnomad4 NFE AF: 0.774

Gnomad4 OTH AF: 0.761

Alfa AF: 0.765 Hom.: 57391

Bravo AF: 0.775

Asia WGS AF: 0.737 AC: 2559 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.34
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1936396; hg19: chr10-45548068; COSMIC: COSV71791018;