rs10484287

Positions:

• chr6-118537016-A-G
• chr6-118537016-A-T

Variant summary

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

The NM_001042475.3(CEP85L):​c.1021-13096T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 151,976 control chromosomes in the GnomAD database, including 38,890 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 0.71 (38890 hom., cov: 31)
• Consequence: CEP85L NM_001042475.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEP85L	NM_001042475.3	c.1021-13096T>C		intron_variant		ENST00000368491.8	NP_001035940.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEP85L	ENST00000368491.8	c.1021-13096T>C		intron_variant		1	NM_001042475.3	ENSP00000357477.3

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107628 AN: 151858 Hom.: 38854 Cov.: 31

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.743

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.709 AC: 107710 AN: 151976 Hom.: 38890 Cov.: 31 AF XY: 0.702 AC XY: 52170 AN XY: 74298

Gnomad4 AFR AF: 0.750

Gnomad4 AMR AF: 0.538

Gnomad4 ASJ AF: 0.700

Gnomad4 EAS AF: 0.353

Gnomad4 SAS AF: 0.664

Gnomad4 FIN AF: 0.743

Gnomad4 NFE AF: 0.749

Gnomad4 OTH AF: 0.668

Alfa AF: 0.743 Hom.: 5249

Bravo AF: 0.689

Asia WGS AF: 0.532 AC: 1847 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.32
DANN	Benign	0.35

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: rs10484287; hg19: chr6-118858179; COSMIC: COSV63827571;