rs10484286

Positions:

• chr6-118635284-T-C

Variant summary

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

The NM_001042475.3(CEP85L):​c.74-2673A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,170 control chromosomes in the GnomAD database, including 1,728 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 0.13 (1728 hom., cov: 32)
• Consequence: CEP85L NM_001042475.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0820

Genes affected

CEP85L (HGNC:21638): (centrosomal protein 85 like) The protein encoded by this gene was identified as a breast cancer antigen. Nothing more is known of its function at this time. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2010]

ACMG classification

Verdict is Benign. Variant got -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 = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEP85L	NM_001042475.3	c.74-2673A>G		intron_variant		ENST00000368491.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP85L	ENST00000368491.8	c.74-2673A>G		intron_variant		1	NM_001042475.3	P1

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20292 AN: 152052 Hom.: 1726 Cov.: 32

Gnomad AFR AF: 0.0319

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.0452

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.133 AC: 20302 AN: 152170 Hom.: 1728 Cov.: 32 AF XY: 0.135 AC XY: 10038 AN XY: 74384

Gnomad4 AFR AF: 0.0320

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.0451

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.143

Alfa AF: 0.167 Hom.: 300

Bravo AF: 0.123

Asia WGS AF: 0.0910 AC: 315 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.74

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

Publications

LitVar

Other links and lift over

dbSNP: rs10484286; hg19: chr6-118956447;