11-47158278-A-G

Variant names:

• chr11-47158278-A-G
• rs1060573
• NM_024113.5:c.757+356A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_024113.5(CSTPP1):​c.757+356A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.649 in 151,992 control chromosomes in the GnomAD database, including 32,458 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 0.65 (32458 hom., cov: 31)
• Consequence: CSTPP1 NM_024113.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.83
• Publications: 18 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.67 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.757+356A>G		intron	N/A	NP_077018.1
	CSTPP1	NM_001003677.3		c.757+356A>G		intron	N/A	NP_001003677.1
	CSTPP1	NM_001003678.3		c.757+356A>G		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.757+356A>G		intron	N/A	ENSP00000278460.8
	CSTPP1	ENST00000378615.7	TSL:1	c.757+356A>G		intron	N/A	ENSP00000367878.3
	CSTPP1	ENST00000395460.6	TSL:1	c.757+356A>G		intron	N/A	ENSP00000378844.2

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98612 AN: 151874 Hom.: 32451 Cov.: 31

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.710

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.649 AC: 98654 AN: 151992 Hom.: 32458 Cov.: 31 AF XY: 0.643 AC XY: 47764 AN XY: 74282

African (AFR) AF: 0.665 AC: 27556 AN: 41444

American (AMR) AF: 0.625 AC: 9548 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.731 AC: 2537 AN: 3470

East Asian (EAS) AF: 0.295 AC: 1524 AN: 5174

South Asian (SAS) AF: 0.663 AC: 3186 AN: 4808

European-Finnish (FIN) AF: 0.583 AC: 6141 AN: 10532

Middle Eastern (MID) AF: 0.705 AC: 206 AN: 292

European-Non Finnish (NFE) AF: 0.675 AC: 45879 AN: 67968

Other (OTH) AF: 0.684 AC: 1445 AN: 2114

Alfa AF: 0.678 Hom.: 55906

Bravo AF: 0.650

Asia WGS AF: 0.561 AC: 1955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	14
DANN	Benign	0.86
PhyloP100		1.8
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: rs1060573; hg19: chr11-47179829;