17-64510162-T-C

Position:

• chr17-64510162-T-C

Variant summary

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

The NM_138363.3(CEP95):​c.149-11T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0554 in 1,446,602 control chromosomes in the GnomAD database, including 4,562 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 0.13 (2188 hom., cov: 31)
  • Exomes 𝑓: 0.047 (2374 hom.)
• Consequence: CEP95 NM_138363.3 intron
• Scores: Splicing: ADA: 0.00009177
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

Genes affected

CEP95 (HGNC:25141): (centrosomal protein 95) Located in centrosome and spindle pole. [provided by Alliance of Genome Resources, Apr 2022]

CEP95 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEP95	NM_138363.3	c.149-11T>C		intron_variant		ENST00000556440.7	NP_612372.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEP95	ENST00000556440.7	c.149-11T>C		intron_variant		1	NM_138363.3	ENSP00000450461.2

Frequencies

GnomAD3 genomes AF: 0.127 AC: 18875 AN: 148834 Hom.: 2178 Cov.: 31

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.0356

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.0453

Gnomad EAS AF: 0.0394

Gnomad SAS AF: 0.0359

Gnomad FIN AF: 0.0456

Gnomad MID AF: 0.0705

Gnomad NFE AF: 0.0423

Gnomad OTH AF: 0.0948

GnomAD3 exomes AF: 0.0722 AC: 14806 AN: 205170 Hom.: 922 AF XY: 0.0638 AC XY: 7052 AN XY: 110540

Gnomad AFR exome AF: 0.295

Gnomad AMR exome AF: 0.156

Gnomad ASJ exome AF: 0.0403

Gnomad EAS exome AF: 0.0409

Gnomad SAS exome AF: 0.0341

Gnomad FIN exome AF: 0.0476

Gnomad NFE exome AF: 0.0402

Gnomad OTH exome AF: 0.0608

GnomAD4 exome AF: 0.0472 AC: 61284 AN: 1297664 Hom.: 2374 Cov.: 21 AF XY: 0.0458 AC XY: 29789 AN XY: 649790

Gnomad4 AFR exome AF: 0.282

Gnomad4 AMR exome AF: 0.150

Gnomad4 ASJ exome AF: 0.0402

Gnomad4 EAS exome AF: 0.0396

Gnomad4 SAS exome AF: 0.0329

Gnomad4 FIN exome AF: 0.0479

Gnomad4 NFE exome AF: 0.0370

Gnomad4 OTH exome AF: 0.0552

GnomAD4 genome AF: 0.127 AC: 18921 AN: 148938 Hom.: 2188 Cov.: 31 AF XY: 0.127 AC XY: 9199 AN XY: 72710

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.0453

Gnomad4 EAS AF: 0.0394

Gnomad4 SAS AF: 0.0362

Gnomad4 FIN AF: 0.0456

Gnomad4 NFE AF: 0.0423

Gnomad4 OTH AF: 0.0938

Alfa AF: 0.0459 Hom.: 56

Bravo AF: 0.141

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.82
DANN	Benign	0.46

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000092
dbscSNV1_RF	Benign	0.0020
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: rs57166100; hg19: chr17-62506280; COSMIC: COSV56748206; COSMIC: COSV56748206;