6-118486684-C-T

Position:

• chr6-118486684-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.1438-2826G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,104 control chromosomes in the GnomAD database, including 2,430 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 0.17 (2430 hom., cov: 32)
• Consequence: CEP85L NM_001042475.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.745

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEP85L	NM_001042475.3	c.1438-2826G>A		intron_variant		ENST00000368491.8
LOC105377971	XR_001743824.3	n.475C>T		non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP85L	ENST00000368491.8	c.1438-2826G>A		intron_variant		1	NM_001042475.3	P1
CEP85L	ENST00000434604.5	c.1447-2826G>A		intron_variant		1
CEP85L	ENST00000368488.9	c.1447-2826G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26497 AN: 151986 Hom.: 2424 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.0517

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.174 AC: 26525 AN: 152104 Hom.: 2430 Cov.: 32 AF XY: 0.175 AC XY: 12992 AN XY: 74336

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.0516

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.179

Alfa AF: 0.186 Hom.: 6083

Bravo AF: 0.169

Asia WGS AF: 0.117 AC: 406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.20
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs25422; hg19: chr6-118807847;