chr1-26242051-T-C

Variant names:

• chr1-26242051-T-C
• rs10902723
• NM_001319944.2:c.56-2115T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001319944.2(CEP85):​c.56-2115T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 151,198 control chromosomes in the GnomAD database, including 22,463 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 (22463 hom., cov: 31)
• Consequence: CEP85 NM_001319944.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.72
• Publications: 10 publications found

Genes affected

CEP85 (HGNC:25309): (centrosomal protein 85) This gene encodes a protein that belongs to the centrosome-associated family of proteins. The centrosome is a subcellular organelle in the animal cell that functions as a microtubule organizing center and is involved in cell-cycle progression. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEP85	NM_001319944.2	c.56-2115T>C		intron_variant	Intron 2 of 13	ENST00000451429.8	NP_001306873.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEP85	ENST00000451429.8	c.56-2115T>C		intron_variant	Intron 2 of 13	2	NM_001319944.2	ENSP00000417002.3
CEP85	ENST00000252992.8	c.56-2115T>C		intron_variant	Intron 2 of 13	1		ENSP00000252992.4
CEP85	ENST00000640292.2	c.55+2213T>C		intron_variant	Intron 2 of 12	5		ENSP00000492362.2

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80254 AN: 151076 Hom.: 22457 Cov.: 31

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.531 AC: 80290 AN: 151198 Hom.: 22463 Cov.: 31 AF XY: 0.520 AC XY: 38442 AN XY: 73876

African (AFR) AF: 0.395 AC: 16272 AN: 41192

American (AMR) AF: 0.468 AC: 7108 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2131 AN: 3464

East Asian (EAS) AF: 0.291 AC: 1472 AN: 5060

South Asian (SAS) AF: 0.329 AC: 1549 AN: 4714

European-Finnish (FIN) AF: 0.591 AC: 6186 AN: 10472

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.644 AC: 43691 AN: 67818

Other (OTH) AF: 0.532 AC: 1118 AN: 2102

Alfa AF: 0.550 Hom.: 5314

Bravo AF: 0.518

Asia WGS AF: 0.299 AC: 1041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.39
DANN	Benign	0.37
PhyloP100		-2.7
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs10902723; hg19: chr1-26568542;