GeneBe

NM_006017.3:c.2583-10dupT

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP6_Moderate

The NM_006017.3(PROM1):​c.2583-10dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000355 in 1,410,206 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000035 ( 0 hom. )

Consequence

PROM1
NM_006017.3 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.184

Publications

0 publications found
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 Gene-Disease associations (from GenCC):
  • PROM1-related dominant retinopathy
    Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
  • retinal macular dystrophy type 2
    Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
  • PROM1-related recessive retinopathy
    Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
  • retinitis pigmentosa 41
    Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
  • cone-rod dystrophy 12
    Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
  • cone-rod dystrophy
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • retinitis pigmentosa
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • Stargardt disease
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 4-15971091-C-CA is Benign according to our data. Variant chr4-15971091-C-CA is described in ClinVar as Benign. ClinVar VariationId is 2956317.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006017.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
PROM1
NM_006017.3
MANE Select
c.2583-10dupT
intron
N/ANP_006008.1O43490-1
PROM1
NM_001145847.2
c.2556-10dupT
intron
N/ANP_001139319.1O43490-2
PROM1
NM_001145848.2
c.2556-10dupT
intron
N/ANP_001139320.1O43490-2

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
PROM1
ENST00000447510.7
TSL:1 MANE Select
c.2583-10dupT
intron
N/AENSP00000415481.2O43490-1
PROM1
ENST00000505450.5
TSL:1
c.2556-10dupT
intron
N/AENSP00000426090.1O43490-2
PROM1
ENST00000508167.5
TSL:1
c.2556-10dupT
intron
N/AENSP00000427346.1O43490-2

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD2 exomes
AF:
0.0000115
AC:
2
AN:
173680
AF XY:
0.0000108
show subpopulations
Gnomad AFR exome
AF:
0.0000988
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000135
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000355
AC:
5
AN:
1410206
Hom.:
0
Cov.:
29
AF XY:
0.00000573
AC XY:
4
AN XY:
697824
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
32200
American (AMR)
AF:
0.00
AC:
0
AN:
38550
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
25390
East Asian (EAS)
AF:
0.00
AC:
0
AN:
37516
South Asian (SAS)
AF:
0.00
AC:
0
AN:
80138
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
45028
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5710
European-Non Finnish (NFE)
AF:
0.00000460
AC:
5
AN:
1087018
Other (OTH)
AF:
0.00
AC:
0
AN:
58656
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.455
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
33

ClinVar

ClinVar submissions
Significance:Benign
Revision:criteria provided, single submitter
View on ClinVar
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (1)

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
-0.18

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs767545051; hg19: chr4-15972714; COSMIC: COSV71699674; COSMIC: COSV71699674; API