14-104880570-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001112726.3(CEP170B):​c.472+145T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 1,216,164 control chromosomes in the GnomAD database, including 249,135 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 0.60 (28318 hom., cov: 32)
  • Exomes 𝑓: 0.64 (220817 hom.)
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CEP170B	NM_001112726.3	c.472+145T>C		intron_variant	Intron 6 of 18	ENST00000414716.8	NP_001106197.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEP170B	ENST00000414716.8	c.472+145T>C		intron_variant	Intron 6 of 18	1	NM_001112726.3	ENSP00000404151.2
CEP170B	ENST00000556508.5	c.262+145T>C		intron_variant	Intron 5 of 17	5		ENSP00000451249.1

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91371 AN: 151550 Hom.: 28310 Cov.: 32

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.634

GnomAD4 exome AF: 0.636 AC: 676967 AN: 1064496 Hom.: 220817 AF XY: 0.635 AC XY: 334100 AN XY: 525768

African (AFR) AF: 0.524 AC: 13136 AN: 25080

American (AMR) AF: 0.553 AC: 15601 AN: 28210

Ashkenazi Jewish (ASJ) AF: 0.700 AC: 13249 AN: 18926

East Asian (EAS) AF: 0.177 AC: 5977 AN: 33788

South Asian (SAS) AF: 0.611 AC: 38315 AN: 62674

European-Finnish (FIN) AF: 0.661 AC: 21423 AN: 32394

Middle Eastern (MID) AF: 0.721 AC: 2323 AN: 3220

European-Non Finnish (NFE) AF: 0.661 AC: 537893 AN: 813682

Other (OTH) AF: 0.624 AC: 29050 AN: 46522

GnomAD4 genome AF: 0.603 AC: 91411 AN: 151668 Hom.: 28318 Cov.: 32 AF XY: 0.600 AC XY: 44489 AN XY: 74106

African (AFR) AF: 0.531 AC: 21946 AN: 41298

American (AMR) AF: 0.588 AC: 8958 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.703 AC: 2442 AN: 3472

East Asian (EAS) AF: 0.222 AC: 1138 AN: 5136

South Asian (SAS) AF: 0.598 AC: 2881 AN: 4818

European-Finnish (FIN) AF: 0.673 AC: 7112 AN: 10572

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.660 AC: 44782 AN: 67832

Other (OTH) AF: 0.631 AC: 1327 AN: 2104

Alfa AF: 0.622 Hom.: 3541

Bravo AF: 0.592

Asia WGS AF: 0.413 AC: 1442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.18
DANN	Benign	0.60
PhyloP100		-0.33
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		0.97
Mutation Taster		=100/0	polymorphism (auto)

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;