rs11752626

chr6-118467489-G-T

Variant summary

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

The NM_001042475.3(CEP85L):c.2254+1583C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 151,868 control chromosomes in the GnomAD database, including 10,318 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 0.35 (10318 hom., cov: 31)
• Consequence: CEP85L NM_001042475.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.300

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]

LOC105377971 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEP85L	NM_001042475.3	c.2254+1583C>A		intron_variant		ENST00000368491.8
LOC105377971	XR_001743824.3	n.31G>T		non_coding_transcript_exon_variant	1/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP85L	ENST00000368491.8	c.2254+1583C>A		intron_variant		1	NM_001042475.3	P1
CEP85L	ENST00000368488.9	c.2263+1583C>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53184 AN: 151752 Hom.: 10318 Cov.: 31

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.350 AC: 53200 AN: 151868 Hom.: 10318 Cov.: 31 AF XY: 0.346 AC XY: 25666 AN XY: 74172

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.367

Gnomad4 EAS AF: 0.282

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.434

Gnomad4 NFE AF: 0.455

Gnomad4 OTH AF: 0.320

Alfa AF: 0.415 Hom.: 2796

Bravo AF: 0.330

Asia WGS AF: 0.304 AC: 1056 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.1
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11752626; hg19: chr6-118788652; COSMIC: COSV63824108;