4-15968578-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006017.3(PROM1):​c.*815C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.859 in 152,256 control chromosomes in the GnomAD database, including 56,807 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 0.86 ( 56807 hom., cov: 33)
Failed GnomAD Quality Control

Consequence

PROM1
NM_006017.3 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0180
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]
FGFBP2 (HGNC:29451): (fibroblast growth factor binding protein 2) This gene encodes a member of the fibroblast growth factor binding protein family. The encoded protein is a serum protein that is selectively secreted by cytotoxic lymphocytes and may be involved in cytotoxic lymphocyte-mediated immunity. An increase in the amount of gene product may be associated with atopic asthma and mild extrinsic asthma.[provided by RefSeq Staff, Oct 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PROM1NM_006017.3 linkc.*815C>G 3_prime_UTR_variant Exon 28 of 28 ENST00000447510.7 NP_006008.1 O43490-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PROM1ENST00000447510 linkc.*815C>G 3_prime_UTR_variant Exon 28 of 28 1 NM_006017.3 ENSP00000415481.2 O43490-1

Frequencies

GnomAD3 genomes
AF:
0.859
AC:
130750
AN:
152138
Hom.:
56774
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.725
Gnomad AMI
AF:
0.986
Gnomad AMR
AF:
0.899
Gnomad ASJ
AF:
0.851
Gnomad EAS
AF:
1.00
Gnomad SAS
AF:
0.953
Gnomad FIN
AF:
0.931
Gnomad MID
AF:
0.905
Gnomad NFE
AF:
0.902
Gnomad OTH
AF:
0.851
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AC:
0
AN:
0
Hom.:
0
Cov.:
0
AC XY:
0
AN XY:
0
GnomAD4 genome
AF:
0.859
AC:
130845
AN:
152256
Hom.:
56807
Cov.:
33
AF XY:
0.865
AC XY:
64388
AN XY:
74458
show subpopulations
Gnomad4 AFR
AF:
0.725
Gnomad4 AMR
AF:
0.899
Gnomad4 ASJ
AF:
0.851
Gnomad4 EAS
AF:
1.00
Gnomad4 SAS
AF:
0.953
Gnomad4 FIN
AF:
0.931
Gnomad4 NFE
AF:
0.903
Gnomad4 OTH
AF:
0.851
Alfa
AF:
0.883
Hom.:
3455
Bravo
AF:
0.849
Asia WGS
AF:
0.966
AC:
3357
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
2.8
DANN
Benign
0.42

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.040
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.

Other links and lift over

dbSNP: rs7686732; hg19: chr4-15970201; API