NM_001042475.3:c.74-3053T>A

Variant names:

• chr6-118635664-A-T
• rs9320660
• NM_001042475.3:c.74-3053T>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001042475.3(CEP85L):​c.74-3053T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,206 control chromosomes in the GnomAD database, including 2,163 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 0.16 (2163 hom., cov: 33)
• Consequence: CEP85L NM_001042475.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEP85L	NM_001042475.3	c.74-3053T>A		intron_variant	Intron 1 of 12	ENST00000368491.8	NP_001035940.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEP85L	ENST00000368491.8	c.74-3053T>A		intron_variant	Intron 1 of 12	1	NM_001042475.3	ENSP00000357477.3

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24888 AN: 152088 Hom.: 2156 Cov.: 33

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.0511

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.164 AC: 24918 AN: 152206 Hom.: 2163 Cov.: 33 AF XY: 0.164 AC XY: 12231 AN XY: 74418

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.0510

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.169

Alfa AF: 0.188 Hom.: 333

Bravo AF: 0.157

Asia WGS AF: 0.115 AC: 401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.0
DANN	Benign	0.51

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

Other links and lift over

dbSNP: rs9320660; hg19: chr6-118956827;