rs7117404

Variant names:

• chr11-47105602-A-G
• rs7117404
• NM_024113.5:c.281-32043A>G

Variant summary

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

The NM_024113.5(CSTPP1):​c.281-32043A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,296 control chromosomes in the GnomAD database, including 1,075 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 0.10 (1075 hom., cov: 32)
• Consequence: CSTPP1 NM_024113.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369
• Publications: 26 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSTPP1	NM_024113.5	c.281-32043A>G		intron_variant	Intron 3 of 8	ENST00000278460.12	NP_077018.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSTPP1	ENST00000278460.12	c.281-32043A>G		intron_variant	Intron 3 of 8	1	NM_024113.5	ENSP00000278460.8

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15682 AN: 152178 Hom.: 1074 Cov.: 32

Gnomad AFR AF: 0.0276

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.0837

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.0468

Gnomad SAS AF: 0.0719

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.103 AC: 15677 AN: 152296 Hom.: 1075 Cov.: 32 AF XY: 0.101 AC XY: 7495 AN XY: 74468

African (AFR) AF: 0.0275 AC: 1145 AN: 41578

American (AMR) AF: 0.0835 AC: 1278 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 861 AN: 3468

East Asian (EAS) AF: 0.0469 AC: 243 AN: 5178

South Asian (SAS) AF: 0.0720 AC: 347 AN: 4822

European-Finnish (FIN) AF: 0.134 AC: 1425 AN: 10608

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9869 AN: 68026

Other (OTH) AF: 0.123 AC: 260 AN: 2108

Alfa AF: 0.136 Hom.: 7046

Bravo AF: 0.0993

Asia WGS AF: 0.0530 AC: 186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.70
DANN	Benign	0.40
PhyloP100		-0.37
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: rs7117404; hg19: chr11-47127153;