Variant rs143998754 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_006017.3(PROM1):c.1454+19_1454+20del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00355 in 1,569,196 control chromosomes in the GnomAD database, including 216 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0049 ( 29 hom., cov: 33)

Exomes 𝑓: 0.0034 ( 187 hom. )

Consequence

PROM1
NM_006017.3 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 1.57

Variant links:

Genes affected

PROM1 (HGNC:9454): (prominin 1) This gene encodes a pentaspan transmembrane glycoprotein. The protein localizes to membrane protrusions and is often expressed on adult stem cells, where it is thought to function in maintaining stem cell properties by suppressing differentiation. Mutations in this gene have been shown to result in retinitis pigmentosa and Stargardt disease. Expression of this gene is also associated with several types of cancer. This gene is expressed from at least five alternative promoters that are expressed in a tissue-dependent manner. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2009]

PROM1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 4-16006517-CAG-C is Benign according to our data. Variant chr4-16006517-CAG-C is described in ClinVar as [Benign]. Clinvar id is 259903.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0996 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PROM1	NM_006017.3 linkuse as main transcript	c.1454+19_1454+20del		intron_variant		ENST00000447510.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PROM1	ENST00000447510.7 linkuse as main transcript	c.1454+19_1454+20del		intron_variant		1	NM_006017.3	P3	O43490-1

Frequencies

GnomAD3 genomes

AF:

0.00488

AC:

743

AN:

152218

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00130

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00327

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.107

Gnomad SAS

AF:

0.0122

Gnomad FIN

AF:

0.0000942

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000191

Gnomad OTH

AF:

0.00478

GnomAD3 exomes

AF:

0.00943

AC:

1786

AN:

189330

Hom.:

AF XY:

0.00888

AC XY:

897

AN XY:

100986

show subpopulations

Gnomad AFR exome

AF:

0.00186

Gnomad AMR exome

AF:

0.00719

Gnomad ASJ exome

AF:

0.000238

Gnomad EAS exome

AF:

0.102

Gnomad SAS exome

AF:

0.00544

Gnomad FIN exome

AF:

0.000112

Gnomad NFE exome

AF:

0.000207

Gnomad OTH exome

AF:

0.00643

GnomAD4 exome

AF:

0.00341

AC:

4836

AN:

1416860

Hom.:

187

AF XY:

0.00350

AC XY:

2451

AN XY:

700302

show subpopulations

Gnomad4 AFR exome

AF:

0.000772

Gnomad4 AMR exome

AF:

0.00665

Gnomad4 ASJ exome

AF:

0.000402

Gnomad4 EAS exome

AF:

0.0948

Gnomad4 SAS exome

AF:

0.00606

Gnomad4 FIN exome

AF:

0.000118

Gnomad4 NFE exome

AF:

0.000108

Gnomad4 OTH exome

AF:

0.00664

GnomAD4 genome

AF:

0.00486

AC:

740

AN:

152336

Hom.:

Cov.:

AF XY:

0.00553

AC XY:

412

AN XY:

74490

show subpopulations

Gnomad4 AFR

AF:

0.00130

Gnomad4 AMR

AF:

0.00327

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.107

Gnomad4 SAS

AF:

0.0118

Gnomad4 FIN

AF:

0.0000942

Gnomad4 NFE

AF:

0.000191

Gnomad4 OTH

AF:

0.00473

Alfa

AF:

0.00160

Hom.:

Bravo

AF:

0.00529

Asia WGS

AF:

0.0390

AC:

136

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Feb 10, 2021	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

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