chr11-46986828-A-G

Variant names:

• chr11-46986828-A-G
• rs7935346
• NM_024113.5:c.47-380A>G

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_024113.5(CSTPP1):​c.47-380A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 152,044 control chromosomes in the GnomAD database, including 31,020 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 0.61 (31020 hom., cov: 31)
• Consequence: CSTPP1 NM_024113.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87
• Publications: 10 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.759 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSTPP1	NM_024113.5	MANE Select	c.47-380A>G		intron	N/A	NP_077018.1	Q9H6J7-1
	CSTPP1	NM_001003677.3		c.47-380A>G		intron	N/A	NP_001003677.1	Q9H6J7-2
	CSTPP1	NM_001003678.3		c.47-380A>G		intron	N/A	NP_001003678.1	Q9H6J7-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSTPP1	ENST00000278460.12	TSL:1 MANE Select	c.47-380A>G		intron	N/A	ENSP00000278460.8	Q9H6J7-1
	CSTPP1	ENST00000378615.7	TSL:1	c.47-380A>G		intron	N/A	ENSP00000367878.3	Q9H6J7-2
	CSTPP1	ENST00000395460.6	TSL:1	c.47-380A>G		intron	N/A	ENSP00000378844.2	Q9H6J7-3

Frequencies

GnomAD3 genomes AF: 0.607 AC: 92182 AN: 151926 Hom.: 31009 Cov.: 31

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.705

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.804

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.607 AC: 92226 AN: 152044 Hom.: 31020 Cov.: 31 AF XY: 0.603 AC XY: 44821 AN XY: 74320

African (AFR) AF: 0.314 AC: 13024 AN: 41468

American (AMR) AF: 0.645 AC: 9844 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.804 AC: 2790 AN: 3468

East Asian (EAS) AF: 0.344 AC: 1781 AN: 5172

South Asian (SAS) AF: 0.706 AC: 3400 AN: 4816

European-Finnish (FIN) AF: 0.678 AC: 7163 AN: 10562

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.765 AC: 51993 AN: 67982

Other (OTH) AF: 0.658 AC: 1383 AN: 2102

Alfa AF: 0.734 Hom.: 71207

Bravo AF: 0.587

Asia WGS AF: 0.600 AC: 2090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.030
DANN	Benign	0.32
PhyloP100		-1.9
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.27		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.27		Position offset: -1

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

Other links and lift over

dbSNP: rs7935346; hg19: chr11-47008379;