rs35407905

chr6-118569065-G-Achr6-118569065-G-C

Variant summary

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

The NM_001042475.3(CEP85L):c.233-2749C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0562 in 151,858 control chromosomes in the GnomAD database, including 290 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 0.056 (290 hom., cov: 31)
• Consequence: CEP85L NM_001042475.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEP85L	NM_001042475.3	c.233-2749C>T		intron_variant		ENST00000368491.8
LOC107986524	XR_007059725.1	n.90+3295G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP85L	ENST00000368491.8	c.233-2749C>T		intron_variant		1	NM_001042475.3	P1
	ENST00000659521.1	n.111+3295G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0563 AC: 8543 AN: 151744 Hom.: 292 Cov.: 31

Gnomad AFR AF: 0.0529

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0319

Gnomad ASJ AF: 0.0481

Gnomad EAS AF: 0.0198

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0651

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0628

Gnomad OTH AF: 0.0535

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

GnomAD4 genome AF: 0.0562 AC: 8536 AN: 151858 Hom.: 290 Cov.: 31 AF XY: 0.0566 AC XY: 4200 AN XY: 74208

Gnomad4 AFR AF: 0.0527

Gnomad4 AMR AF: 0.0318

Gnomad4 ASJ AF: 0.0481

Gnomad4 EAS AF: 0.0199

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.0651

Gnomad4 NFE AF: 0.0628

Gnomad4 OTH AF: 0.0530

Alfa AF: 0.0289 Hom.: 15

Bravo AF: 0.0500

Asia WGS AF: 0.0540 AC: 187 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.74
Dann	Benign	0.42

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: rs35407905; hg19: chr6-118890228;