6-118558626-TACAC-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_001042475.3(CEP85L):​c.1020+6899_1020+6902delGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.25 ( 3446 hom., cov: 0)
Failed GnomAD Quality Control

Consequence

CEP85L
NM_001042475.3 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.379
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]
PLN (HGNC:9080): (phospholamban) The protein encoded by this gene is found as a pentamer and is a major substrate for the cAMP-dependent protein kinase in cardiac muscle. The encoded protein is an inhibitor of cardiac muscle sarcoplasmic reticulum Ca(2+)-ATPase in the unphosphorylated state, but inhibition is relieved upon phosphorylation of the protein. The subsequent activation of the Ca(2+) pump leads to enhanced muscle relaxation rates, thereby contributing to the inotropic response elicited in heart by beta-agonists. The encoded protein is a key regulator of cardiac diastolic function. Mutations in this gene are a cause of inherited human dilated cardiomyopathy with refractory congestive heart failure, and also familial hypertrophic cardiomyopathy. [provided by RefSeq, Apr 2016]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

BP6
Variant 6-118558626-TACAC-T is Benign according to our data. Variant chr6-118558626-TACAC-T is described in ClinVar as [Benign]. Clinvar id is 1252105.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CEP85LNM_001042475.3 linkc.1020+6899_1020+6902delGTGT intron_variant ENST00000368491.8 NP_001035940.1 Q5SZL2-1Q3ZCQ5
PLNNM_002667.5 linkc.-97-167_-97-164delCACA intron_variant ENST00000357525.6 NP_002658.1 P26678Q5R352

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CEP85LENST00000368491.8 linkc.1020+6899_1020+6902delGTGT intron_variant 1 NM_001042475.3 ENSP00000357477.3 Q5SZL2-1
PLNENST00000357525.6 linkc.-97-198_-97-195delACAC intron_variant 1 NM_002667.5 ENSP00000350132.5 P26678

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
27294
AN:
111282
Hom.:
3443
Cov.:
0
FAILED QC
Gnomad AFR
AF:
0.147
Gnomad AMI
AF:
0.242
Gnomad AMR
AF:
0.398
Gnomad ASJ
AF:
0.272
Gnomad EAS
AF:
0.526
Gnomad SAS
AF:
0.293
Gnomad FIN
AF:
0.338
Gnomad MID
AF:
0.243
Gnomad NFE
AF:
0.236
Gnomad OTH
AF:
0.277
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.245
AC:
27304
AN:
111348
Hom.:
3446
Cov.:
0
AF XY:
0.255
AC XY:
13265
AN XY:
52086
show subpopulations
Gnomad4 AFR
AF:
0.147
Gnomad4 AMR
AF:
0.398
Gnomad4 ASJ
AF:
0.272
Gnomad4 EAS
AF:
0.526
Gnomad4 SAS
AF:
0.294
Gnomad4 FIN
AF:
0.338
Gnomad4 NFE
AF:
0.236
Gnomad4 OTH
AF:
0.278

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxAug 21, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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

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

Other links and lift over

dbSNP: rs371775061; hg19: chr6-118879789; API