rs11600292

Variant names:

• chr11-46937147-T-C
• rs11600292
• NM_024113.5:c.46+296T>C

Variant summary

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

The NM_024113.5(CSTPP1):​c.46+296T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,138 control chromosomes in the GnomAD database, including 5,115 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 0.24 (5115 hom., cov: 32)
• Consequence: CSTPP1 NM_024113.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.322
• Publications: 9 publications found

Genes affected

CSTPP1 (HGNC:28720): (centriolar satellite-associated tubulin polyglutamylase complex regulator 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.635 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024113.5. 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
	CSTPP1	NM_024113.5	MANE Select	c.46+296T>C		intron	N/A	NP_077018.1
	CSTPP1	NM_001003677.3		c.46+296T>C		intron	N/A	NP_001003677.1
	CSTPP1	NM_001003678.3		c.46+296T>C		intron	N/A	NP_001003678.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSTPP1	ENST00000278460.12	TSL:1 MANE Select	c.46+296T>C		intron	N/A	ENSP00000278460.8
	CSTPP1	ENST00000378615.7	TSL:1	c.46+296T>C		intron	N/A	ENSP00000367878.3
	CSTPP1	ENST00000395460.6	TSL:1	c.46+296T>C		intron	N/A	ENSP00000378844.2

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36522 AN: 152020 Hom.: 5107 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.240 AC: 36554 AN: 152138 Hom.: 5115 Cov.: 32 AF XY: 0.248 AC XY: 18464 AN XY: 74366

African (AFR) AF: 0.157 AC: 6523 AN: 41524

American (AMR) AF: 0.302 AC: 4613 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 596 AN: 3466

East Asian (EAS) AF: 0.654 AC: 3368 AN: 5152

South Asian (SAS) AF: 0.291 AC: 1402 AN: 4814

European-Finnish (FIN) AF: 0.320 AC: 3389 AN: 10582

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15890 AN: 67998

Other (OTH) AF: 0.215 AC: 455 AN: 2114

Alfa AF: 0.223 Hom.: 2759

Bravo AF: 0.240

Asia WGS AF: 0.373 AC: 1295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	10
DANN	Benign	0.57
PhyloP100		0.32
PromoterAI		0.094	Neutral
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: rs11600292; hg19: chr11-46958698;