11-47154454-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

LOC124902672 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSTPP1	NM_024113.5	c.366-722C>T		intron_variant		ENST00000278460.12
LOC124902672	XR_007062668.1	n.314G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSTPP1	ENST00000278460.12	c.366-722C>T		intron_variant		1	NM_024113.5	P3

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

Gnomad4 AMR exome AF: 0.500

Gnomad4 FIN exome AF: 0.563

Gnomad4 NFE exome AF: 0.245

Gnomad4 OTH exome AF: 0.167

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

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.371

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.706

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.417

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.305

Alfa AF: 0.299 Hom.: 6884

Bravo AF: 0.339

Asia WGS AF: 0.434 AC: 1504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	1.4
Dann	Benign	0.80

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

Publications

LitVar

Other links and lift over

dbSNP: rs747650; hg19: chr11-47176005;