rs2677780

chr4-16020917-G-Achr4-16020917-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006017.3(PROM1):c.785-2377C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.899 in 152,240 control chromosomes in the GnomAD database, including 61,809 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 0.90 (61809 hom., cov: 32)
• Consequence: PROM1 NM_006017.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.932 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PROM1	NM_006017.3	c.785-2377C>T		intron_variant		ENST00000447510.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PROM1	ENST00000447510.7	c.785-2377C>T		intron_variant		1	NM_006017.3	P3

Frequencies

GnomAD3 genomes AF: 0.899 AC: 136700 AN: 152122 Hom.: 61748 Cov.: 32

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.922

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.946

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.933

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.938

Gnomad OTH AF: 0.905

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.899 AC: 136822 AN: 152240 Hom.: 61809 Cov.: 32 AF XY: 0.893 AC XY: 66445 AN XY: 74432

Gnomad4 AFR AF: 0.883

Gnomad4 AMR AF: 0.811

Gnomad4 ASJ AF: 0.946

Gnomad4 EAS AF: 0.710

Gnomad4 SAS AF: 0.836

Gnomad4 FIN AF: 0.933

Gnomad4 NFE AF: 0.938

Gnomad4 OTH AF: 0.906

Alfa AF: 0.915 Hom.: 10538

Bravo AF: 0.892

Asia WGS AF: 0.755 AC: 2629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	5.2
Dann	Benign	0.15

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		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

Other links and lift over

dbSNP: rs2677780; hg19: chr4-16022540;