ENST00000337471.8:n.1454-8371G>A

Variant names:

• chr22-22003803-C-T
• rs6000509
• ENST00000337471.8:n.1454-8371G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000337471.8(PRAMENP):​n.1454-8371G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0803 in 151,812 control chromosomes in the GnomAD database, including 688 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 0.080 (688 hom., cov: 31)
• Consequence: PRAMENP ENST00000337471.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 4 publications found

Genes affected

PRAMENP (HGNC:):

PRAMENP (HGNC:34302): (PRAME N-terminal like, pseudogene)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000337471.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRAMENP	NR_135291.1		n.1454-8371G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRAMENP	ENST00000337471.8	TSL:2	n.1454-8371G>A		intron	N/A
	PRAMENP	ENST00000419303.5	TSL:2	n.284-8371G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0801 AC: 12157 AN: 151694 Hom.: 682 Cov.: 31

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.0209

Gnomad AMR AF: 0.0850

Gnomad ASJ AF: 0.0664

Gnomad EAS AF: 0.0203

Gnomad SAS AF: 0.0884

Gnomad FIN AF: 0.0532

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0439

Gnomad OTH AF: 0.0872

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

GnomAD4 genome AF: 0.0803 AC: 12197 AN: 151812 Hom.: 688 Cov.: 31 AF XY: 0.0808 AC XY: 5992 AN XY: 74180

African (AFR) AF: 0.154 AC: 6375 AN: 41370

American (AMR) AF: 0.0853 AC: 1299 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.0664 AC: 230 AN: 3464

East Asian (EAS) AF: 0.0201 AC: 104 AN: 5170

South Asian (SAS) AF: 0.0879 AC: 420 AN: 4780

European-Finnish (FIN) AF: 0.0532 AC: 561 AN: 10548

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0438 AC: 2979 AN: 67950

Other (OTH) AF: 0.0863 AC: 182 AN: 2108

Alfa AF: 0.0602 Hom.: 1019

Bravo AF: 0.0841

Asia WGS AF: 0.0950 AC: 329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.9
DANN	Benign	0.75
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs6000509; hg19: chr22-22358201;