6-118558626-TACACACACACACACACACAC-TACACACACACACACAC

Variant names:

• chr6-118558626-TACAC-T
• rs371775061
• NM_001042475.3:c.1020+6899_1020+6902delGTGT

Variant summary

Our verdict is Likely benign. The variant received -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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.379
• Publications: 0 publications found

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]

PLN Gene-Disease associations (from GenCC):

• dilated cardiomyopathy 1P

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
• intrinsic cardiomyopathy

  Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
• hypertrophic cardiomyopathy 18

  Inheritance: AD Classification: STRONG, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
• arrhythmogenic right ventricular cardiomyopathy

  Inheritance: AD Classification: MODERATE Submitted by: ClinGen
• familial isolated dilated cardiomyopathy

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Likely_benign. The variant received -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 VariationId is 1252105.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001042475.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEP85L	NM_001042475.3	MANE Select	c.1020+6899_1020+6902delGTGT		intron	N/A	NP_001035940.1	Q5SZL2-1
	PLN	NM_002667.5	MANE Select	c.-97-167_-97-164delCACA		intron	N/A	NP_002658.1	P26678
	CEP85L	NM_001178035.2		c.1029+6899_1029+6902delGTGT		intron	N/A	NP_001171506.1	Q5SZL2-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEP85L	ENST00000368491.8	TSL:1 MANE Select	c.1020+6899_1020+6902delGTGT		intron	N/A	ENSP00000357477.3	Q5SZL2-1
	PLN	ENST00000357525.6	TSL:1 MANE Select	c.-97-198_-97-195delACAC		intron	N/A	ENSP00000350132.5	P26678
	CEP85L	ENST00000434604.5	TSL:1	c.1029+6899_1029+6902delGTGT		intron	N/A	ENSP00000392131.1	A2A3P3

Frequencies

GnomAD3 genomes AF: 0.245 AC: 27294 AN: 111282 Hom.: 3443 Cov.: 0

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

African (AFR) AF: 0.147 AC: 4507 AN: 30728

American (AMR) AF: 0.398 AC: 4421 AN: 11096

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 783 AN: 2876

East Asian (EAS) AF: 0.526 AC: 2097 AN: 3990

South Asian (SAS) AF: 0.294 AC: 769 AN: 2612

European-Finnish (FIN) AF: 0.338 AC: 1623 AN: 4804

Middle Eastern (MID) AF: 0.236 AC: 49 AN: 208

European-Non Finnish (NFE) AF: 0.236 AC: 12460 AN: 52798

Other (OTH) AF: 0.278 AC: 418 AN: 1504

Alfa AF: 0.180 Hom.: 143

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.38
Mutation Taster		=100/0	polymorphism (auto)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs371775061;

hg19: chr6-118879789;