NM_138363.3:c.149-11T>G

Variant names:

• chr17-64510162-T-G
• rs57166100
• NM_138363.3:c.149-11T>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_138363.3(CEP95):​c.149-11T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000231 in 1,299,176 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0000023 (0 hom.)
• Consequence: CEP95 NM_138363.3 intron
• Scores: Splicing: ADA: 0.0006716
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138363.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEP95	NM_138363.3	MANE Select	c.149-11T>G		intron	N/A	NP_612372.1
	CEP95	NM_001316990.2		c.-238-11T>G		intron	N/A	NP_001303919.1
	CEP95	NR_133644.2		n.270-11T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEP95	ENST00000556440.7	TSL:1 MANE Select	c.149-11T>G		intron	N/A	ENSP00000450461.2
	CEP95	ENST00000553956.6	TSL:1	n.149-11T>G		intron	N/A	ENSP00000452317.2
	CEP95	ENST00000581056.5	TSL:2	c.149-11T>G		intron	N/A	ENSP00000462189.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 0.00000231 AC: 3 AN: 1299176 Hom.: 0 Cov.: 21 AF XY: 0.00000307 AC XY: 2 AN XY: 650482

African (AFR) AF: 0.00 AC: 0 AN: 29706

American (AMR) AF: 0.00 AC: 0 AN: 40578

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 24292

East Asian (EAS) AF: 0.00 AC: 0 AN: 38680

South Asian (SAS) AF: 0.00 AC: 0 AN: 80244

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 51432

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5532

European-Non Finnish (NFE) AF: 0.00000308 AC: 3 AN: 973826

Other (OTH) AF: 0.00 AC: 0 AN: 54886

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.72
DANN	Benign	0.50
PhyloP100		-1.1
PromoterAI		0.015	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.00067
dbscSNV1_RF	Benign	0.090
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs57166100; hg19: chr17-62506280;