Variant chr1-30936879-CCT-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_001020658.2(PUM1):c.3243-46_3243-45delAG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 1,499,110 control chromosomes in the GnomAD database, including 78,898 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.25 ( 5730 hom., cov: 22)

Exomes 𝑓: 0.32 ( 73168 hom. )

Consequence

PUM1
NM_001020658.2 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0500

Variant links:

Genes affected

PUM1 (HGNC:14957): (pumilio RNA binding family member 1) This gene encodes a member of the PUF family, evolutionarily conserved RNA-binding proteins related to the Pumilio proteins of Drosophila and the fem-3 mRNA binding factor proteins of C. elegans. The encoded protein contains a sequence-specific RNA binding domain comprised of eight repeats and N- and C-terminal flanking regions, and serves as a translational regulator of specific mRNAs by binding to their 3' untranslated regions. The evolutionarily conserved function of the encoded protein in invertebrates and lower vertebrates suggests that the human protein may be involved in translational regulation of embryogenesis, and cell development and differentiation. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

PUM1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 1-30936879-CCT-C is Benign according to our data. Variant chr1-30936879-CCT-C is described in ClinVar as [Benign]. Clinvar id is 1232135.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PUM1	NM_001020658.2 link	c.3243-46_3243-45delAG		intron_variant		ENST00000426105.7	NP_001018494.1	Q14671-3
PUM1	NM_014676.3 link	c.3237-46_3237-45delAG		intron_variant			NP_055491.1	Q14671-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PUM1	ENST00000426105.7 link	c.3243-46_3243-45delAG		intron_variant		1	NM_001020658.2	ENSP00000391723.2		Q14671-3

Frequencies

GnomAD3 genomes

AF:

0.247

AC:

37413

AN:

151756

Hom.:

5731

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0821

Gnomad AMI

AF:

0.309

Gnomad AMR

AF:

0.301

Gnomad ASJ

AF:

0.255

Gnomad EAS

AF:

0.00366

Gnomad SAS

AF:

0.250

Gnomad FIN

AF:

0.343

Gnomad MID

AF:

0.263

Gnomad NFE

AF:

0.337

Gnomad OTH

AF:

0.243

GnomAD3 exomes

AF:

0.283

AC:

60967

AN:

215070

Hom.:

9909

AF XY:

0.288

AC XY:

33214

AN XY:

115182

show subpopulations

Gnomad AFR exome

AF:

0.0782

Gnomad AMR exome

AF:

0.324

Gnomad ASJ exome

AF:

0.255

Gnomad EAS exome

AF:

0.00132

Gnomad SAS exome

AF:

0.270

Gnomad FIN exome

AF:

0.356

Gnomad NFE exome

AF:

0.341

Gnomad OTH exome

AF:

0.300

GnomAD4 exome

AF:

0.320

AC:

431113

AN:

1347236

Hom.:

73168

AF XY:

0.319

AC XY:

213239

AN XY:

668778

show subpopulations

Gnomad4 AFR exome

AF:

0.0711

Gnomad4 AMR exome

AF:

0.320

Gnomad4 ASJ exome

AF:

0.245

Gnomad4 EAS exome

AF:

0.00122

Gnomad4 SAS exome

AF:

0.274

Gnomad4 FIN exome

AF:

0.350

Gnomad4 NFE exome

AF:

0.345

Gnomad4 OTH exome

AF:

0.285

GnomAD4 genome

AF:

0.246

AC:

37421

AN:

151874

Hom.:

5730

Cov.:

AF XY:

0.246

AC XY:

18275

AN XY:

74218

show subpopulations

Gnomad4 AFR

AF:

0.0819

Gnomad4 AMR

AF:

0.301

Gnomad4 ASJ

AF:

0.255

Gnomad4 EAS

AF:

0.00386

Gnomad4 SAS

AF:

0.251

Gnomad4 FIN

AF:

0.343

Gnomad4 NFE

AF:

0.337

Gnomad4 OTH

AF:

0.245

Alfa

AF:

0.292

Hom.:

1284

Bravo

AF:

0.235

Asia WGS

AF:

0.116

AC:

405

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 14, 2021

- -

Spinocerebellar ataxia 47

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Nov 07, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over