11-47154454-C-T

Variant names:

• chr11-47154454-C-T
• rs747650
• NM_024113.5:c.366-722C>T

Variant summary

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

The NM_024113.5(CSTPP1):​c.366-722C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 152,036 control chromosomes in the GnomAD database, including 9,294 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 0.34 (9288 hom., cov: 32)
  • Exomes 𝑓: 0.29 (6 hom.)
• Consequence: CSTPP1 NM_024113.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.470
• Publications: 27 publications found

Genes affected

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

LOC124902672 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.686 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.366-722C>T		intron	N/A	NP_077018.1
	CSTPP1	NM_001003677.3		c.366-722C>T		intron	N/A	NP_001003677.1
	CSTPP1	NM_001003678.3		c.366-722C>T		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.366-722C>T		intron	N/A	ENSP00000278460.8
	CSTPP1	ENST00000378615.7	TSL:1	c.366-722C>T		intron	N/A	ENSP00000367878.3
	CSTPP1	ENST00000395460.6	TSL:1	c.366-722C>T		intron	N/A	ENSP00000378844.2

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51647 AN: 151796 Hom.: 9269 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.417

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.311

GnomAD4 exome AF: 0.287 AC: 35 AN: 122 Hom.: 6 Cov.: 0 AF XY: 0.292 AC XY: 21 AN XY: 72

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.563 AC: 9 AN: 16

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.245 AC: 24 AN: 98

Other (OTH) AF: 0.167 AC: 1 AN: 6

GnomAD4 genome AF: 0.340 AC: 51711 AN: 151914 Hom.: 9288 Cov.: 32 AF XY: 0.347 AC XY: 25781 AN XY: 74258

African (AFR) AF: 0.299 AC: 12385 AN: 41410

American (AMR) AF: 0.371 AC: 5669 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 932 AN: 3468

East Asian (EAS) AF: 0.706 AC: 3634 AN: 5150

South Asian (SAS) AF: 0.335 AC: 1613 AN: 4814

European-Finnish (FIN) AF: 0.417 AC: 4390 AN: 10534

Middle Eastern (MID) AF: 0.288 AC: 84 AN: 292

European-Non Finnish (NFE) AF: 0.325 AC: 22080 AN: 67954

Other (OTH) AF: 0.305 AC: 645 AN: 2112

Alfa AF: 0.323 Hom.: 21909

Bravo AF: 0.339

Asia WGS AF: 0.434 AC: 1504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.4
DANN	Benign	0.80
PhyloP100		-0.47
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: rs747650; hg19: chr11-47176005;