6-118469191-A-G

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001042475.3(CEP85L):c.2135T>C(p.Ile712Thr) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: CEP85L NM_001042475.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 4.66

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]

LOC105377971 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.31153512).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEP85L	NM_001042475.3	c.2135T>C	p.Ile712Thr	missense_variant	12/13	ENST00000368491.8
LOC105377971	XR_001743824.3	n.82+1651A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP85L	ENST00000368491.8	c.2135T>C	p.Ile712Thr	missense_variant	12/13	1	NM_001042475.3	P1
CEP85L	ENST00000368488.9	c.2144T>C	p.Ile715Thr	missense_variant	13/14	5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Lissencephaly 10 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Revvity Omics, Revvity

Nov 21, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.099
BayesDel_addAF	Benign	-0.14	T
BayesDel_noAF	Benign	-0.44
Cadd	Benign	21
Dann	Benign	0.95
DEOGEN2	Benign	0.0014	T;.
Eigen	Benign	-0.13
Eigen_PC	Benign	0.12
FATHMM_MKL	Benign	0.27	N
LIST_S2	Benign	0.77	T;T
M_CAP	Benign	0.0084	T
MetaRNN	Benign	0.31	T;T
MetaSVM	Benign	-0.92	T
MutationAssessor	Benign	0.62	N;.
MutationTaster	Benign	0.74	N;N
PrimateAI	Uncertain	0.56	T
PROVEAN	Benign	0.31	N;N
REVEL	Benign	0.15
Sift	Benign	0.40	T;T
Sift4G	Benign	0.49	T;T
Polyphen		0.053	B;.
Vest4		0.55
MutPred		0.29		Loss of stability (P = 0.0029);.;
MVP		0.29
MPC		0.16
ClinPred		0.90	D
GERP RS		6.2
Varity_R		0.082
gMVP		0.14

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr6-118790354;