Variant 4-15963240-G-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The variant allele was found at a frequency of 0.367 in 1,140,408 control chromosomes in the GnomAD database, including 80,783 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 0.33 ( 9386 hom., cov: 33)

Exomes 𝑓: 0.37 ( 71397 hom. )

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.494

Variant links:

Genes affected

(HGNC:):

links:

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.15963240G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PROM1	ENST00000503884.5 linkuse as main transcript	n.*342-81C>A		intron_variant		3		ENSP00000423860.1		H0Y9D4
FGFBP2	ENST00000509331.1 linkuse as main transcript	n.83-2629C>A		intron_variant		2

Frequencies

GnomAD3 genomes

AF:

0.333

AC:

50630

AN:

152020

Hom.:

9377

Cov.:

show subpopulations

Gnomad AFR

AF:

0.176

Gnomad AMI

AF:

0.383

Gnomad AMR

AF:

0.489

Gnomad ASJ

AF:

0.470

Gnomad EAS

AF:

0.294

Gnomad SAS

AF:

0.542

Gnomad FIN

AF:

0.338

Gnomad MID

AF:

0.339

Gnomad NFE

AF:

0.372

Gnomad OTH

AF:

0.371

GnomAD4 exome

AF:

0.372

AC:

367665

AN:

988270

Hom.:

71397

Cov.:

AF XY:

0.378

AC XY:

186078

AN XY:

492534

show subpopulations

Gnomad4 AFR exome

AF:

0.160

Gnomad4 AMR exome

AF:

0.550

Gnomad4 ASJ exome

AF:

0.488

Gnomad4 EAS exome

AF:

0.273

Gnomad4 SAS exome

AF:

0.530

Gnomad4 FIN exome

AF:

0.351

Gnomad4 NFE exome

AF:

0.364

Gnomad4 OTH exome

AF:

0.371

GnomAD4 genome

AF:

0.333

AC:

50659

AN:

152138

Hom.:

9386

Cov.:

AF XY:

0.339

AC XY:

25192

AN XY:

74338

show subpopulations

Gnomad4 AFR

AF:

0.176

Gnomad4 AMR

AF:

0.489

Gnomad4 ASJ

AF:

0.470

Gnomad4 EAS

AF:

0.294

Gnomad4 SAS

AF:

0.544

Gnomad4 FIN

AF:

0.338

Gnomad4 NFE

AF:

0.372

Gnomad4 OTH

AF:

0.370

Alfa

AF:

0.350

Hom.:

4412

Bravo

AF:

0.338

Asia WGS

AF:

0.399

AC:

1391

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

6.3

DANN

Benign

0.73

Splicing

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over