rs2841233

Variant names:

• chr14-104880570-T-A
• rs2841233
• NM_001112726.3:c.472+145T>A

Your query was ambiguous. Multiple possible variants found:

• chr14-104880570-T-A
• chr14-104880570-T-C

Variant summary

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

The NM_001112726.3(CEP170B):​c.472+145T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CEP170B NM_001112726.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.328
• Publications: 10 publications found

Genes affected

CEP170B (HGNC:20362): (centrosomal protein 170B) Predicted to be located in cytoplasm and microtubule. [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=-0.89).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001112726.3. 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
	CEP170B	NM_001112726.3	MANE Select	c.472+145T>A		intron	N/A	NP_001106197.1
	CEP170B	NM_015005.3		c.262+145T>A		intron	N/A	NP_055820.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEP170B	ENST00000414716.8	TSL:1 MANE Select	c.472+145T>A		intron	N/A	ENSP00000404151.2
	CEP170B	ENST00000556508.5	TSL:5	c.262+145T>A		intron	N/A	ENSP00000451249.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1066670 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 526756

African (AFR) AF: 0.00 AC: 0 AN: 25138

American (AMR) AF: 0.00 AC: 0 AN: 28234

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18940

East Asian (EAS) AF: 0.00 AC: 0 AN: 33810

South Asian (SAS) AF: 0.00 AC: 0 AN: 62736

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 32422

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3222

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 815560

Other (OTH) AF: 0.00 AC: 0 AN: 46608

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 3541

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.15
DANN	Benign	0.56
PhyloP100		-0.33
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		0.97

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

Other links and lift over

dbSNP: rs2841233; hg19: chr14-105346907;