rs7759088

Positions:

• chr6-118578206-C-T

Variant summary

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

The NM_001042475.3(CEP85L):​c.233-11890G>A 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 152,016 control chromosomes in the GnomAD database, including 38,958 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 (38958 hom., cov: 31)
• Consequence: CEP85L NM_001042475.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

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]

LOC107986524 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEP85L	NM_001042475.3	c.233-11890G>A		intron_variant		ENST00000368491.8	NP_001035940.1
LOC107986524	XR_007059725.1	n.2251C>T		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEP85L	ENST00000368491.8	c.233-11890G>A		intron_variant		1	NM_001042475.3	ENSP00000357477	P1

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107742 AN: 151898 Hom.: 38922 Cov.: 31

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.743

Gnomad MID AF: 0.774

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.709 AC: 107824 AN: 152016 Hom.: 38958 Cov.: 31 AF XY: 0.703 AC XY: 52236 AN XY: 74326

Gnomad4 AFR AF: 0.751

Gnomad4 AMR AF: 0.538

Gnomad4 ASJ AF: 0.700

Gnomad4 EAS AF: 0.355

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.: 5253

Bravo AF: 0.689

Asia WGS AF: 0.533 AC: 1856 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.29

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: rs7759088; hg19: chr6-118899369;