rs9622750

Variant names:

• chr22-22043373-G-A
• rs9622750

Variant summary

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

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: IGL intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142
• Publications: 2 publications found

Genes affected

IGL (HGNC:5853):

PRAMENP (HGNC:):

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

IGLV10-67 (HGNC:5885): (immunoglobulin lambda variable 10-67 (pseudogene))

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
IGL		n.22043373G>A		intragenic_variant
PRAMENP	NR_135291.1	n.253+309C>T		intron_variant	Intron 1 of 6
IGLV10-67	unassigned_transcript_3556	c.-79G>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRAMENP	ENST00000337471.8	n.253+309C>T		intron_variant	Intron 1 of 6	2
PRAMENP	ENST00000419303.5	n.177+309C>T		intron_variant	Intron 1 of 4	2
IGLV10-67	ENST00000519446.1	n.-245G>A		upstream_gene_variant		6

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

African (AFR) AF: 0.232 AC: 9611 AN: 41470

American (AMR) AF: 0.102 AC: 1554 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0704 AC: 244 AN: 3468

East Asian (EAS) AF: 0.151 AC: 784 AN: 5180

South Asian (SAS) AF: 0.0377 AC: 182 AN: 4826

European-Finnish (FIN) AF: 0.0421 AC: 447 AN: 10614

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 292

European-Non Finnish (NFE) AF: 0.0481 AC: 3272 AN: 67998

Other (OTH) AF: 0.0892 AC: 188 AN: 2108

Alfa AF: 0.0901 Hom.: 192

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
PhyloP100		-0.14
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: rs9622750; hg19: chr22-22397771;