rs9622750

Positions:

• chr22-22043373-G-A

Variant summary

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

The NR_135291.1(PRAMENP):​n.253+309C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,152 control chromosomes in the GnomAD database, including 1,411 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 0.11 (1411 hom., cov: 32)
• Consequence: PRAMENP NR_135291.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142

Genes affected

PRAMENP (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRAMENP	NR_135291.1	n.253+309C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRAMENP	ENST00000337471.8	n.253+309C>T		intron_variant, non_coding_transcript_variant		2
PRAMENP	ENST00000419303.5	n.177+309C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16398 AN: 152038 Hom.: 1403 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0704

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.0383

Gnomad FIN AF: 0.0421

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0481

Gnomad OTH AF: 0.0906

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

GnomAD4 genome AF: 0.108 AC: 16425 AN: 152152 Hom.: 1411 Cov.: 32 AF XY: 0.106 AC XY: 7896 AN XY: 74400

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.0704

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.0377

Gnomad4 FIN AF: 0.0421

Gnomad4 NFE AF: 0.0481

Gnomad4 OTH AF: 0.0892

Alfa AF: 0.0856 Hom.: 166

Bravo AF: 0.121

Asia WGS AF: 0.127 AC: 442 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.8
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9622750; hg19: chr22-22397771;