Variant chr6-118672469-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000434604.5(CEP85L):c.-27-19661G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 151,784 control chromosomes in the GnomAD database, including 13,262 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 0.41 ( 13262 hom., cov: 33)

Consequence

CEP85L
ENST00000434604.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.305

Variant links:

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]

CEP85L links:

LOC124901388 (HGNC:):

LOC124901388 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901388	XR_007059727.1 linkuse as main transcript	n.344+7319C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	UniProt
CEP85L	ENST00000392500.7 linkuse as main transcript	c.-138-7948G>T	intron_variant	1	Q5SZL2-2
CEP85L	ENST00000434604.5 linkuse as main transcript	c.-27-19661G>T	intron_variant	1
CEP85L	ENST00000368488.9 linkuse as main transcript	c.-27-19661G>T	intron_variant	5	Q5SZL2-4

Frequencies

GnomAD3 genomes

AF:

0.414

AC:

62854

AN:

151668

Hom.:

13254

Cov.:

show subpopulations

Gnomad AFR

AF:

0.382

Gnomad AMI

AF:

0.430

Gnomad AMR

AF:

0.309

Gnomad ASJ

AF:

0.367

Gnomad EAS

AF:

0.275

Gnomad SAS

AF:

0.373

Gnomad FIN

AF:

0.443

Gnomad MID

AF:

0.513

Gnomad NFE

AF:

0.470

Gnomad OTH

AF:

0.382

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

GnomAD4 genome

AF:

0.414

AC:

62888

AN:

151784

Hom.:

13262

Cov.:

AF XY:

0.408

AC XY:

30283

AN XY:

74166

show subpopulations

Gnomad4 AFR

AF:

0.382

Gnomad4 AMR

AF:

0.308

Gnomad4 ASJ

AF:

0.367

Gnomad4 EAS

AF:

0.275

Gnomad4 SAS

AF:

0.373

Gnomad4 FIN

AF:

0.443

Gnomad4 NFE

AF:

0.470

Gnomad4 OTH

AF:

0.382

Alfa

AF:

0.446

Hom.:

2462

Bravo

AF:

0.404

Asia WGS

AF:

0.318

AC:

1103

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.63

DANN

Benign

0.47

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over