rs8137446

Variant names:

• chr22-36951918-C-T
• rs8137446

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 0.179 in 151,752 control chromosomes in the GnomAD database, including 2,787 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 0.18 (2787 hom., cov: 31)
• Consequence: CSF2RBP1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662
• Publications: 8 publications found

Genes affected

CSF2RBP1 (HGNC:2437): (CSF2RB pseudogene 1)

ENSG00000309254 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSF2RBP1		n.36951918C>T		intragenic_variant
LOC124900478	XR_007068091.1	n.1014-820G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSF2RBP1	ENST00000447905.1	n.200+994G>A		intron_variant	Intron 2 of 2	6
ENSG00000309254	ENST00000839834.1	n.389-820G>A		intron_variant	Intron 2 of 3
ENSG00000309254	ENST00000839835.1	n.1014-820G>A		intron_variant	Intron 1 of 2
ENSG00000309254	ENST00000839836.1	n.352-1075G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27120 AN: 151632 Hom.: 2777 Cov.: 31

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.0440

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.179 AC: 27148 AN: 151752 Hom.: 2787 Cov.: 31 AF XY: 0.183 AC XY: 13582 AN XY: 74148

African (AFR) AF: 0.215 AC: 8890 AN: 41366

American (AMR) AF: 0.246 AC: 3750 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 520 AN: 3464

East Asian (EAS) AF: 0.213 AC: 1093 AN: 5128

South Asian (SAS) AF: 0.376 AC: 1806 AN: 4808

European-Finnish (FIN) AF: 0.140 AC: 1473 AN: 10530

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9088 AN: 67928

Other (OTH) AF: 0.201 AC: 420 AN: 2088

Alfa AF: 0.153 Hom.: 4459

Bravo AF: 0.184

Asia WGS AF: 0.306 AC: 1060 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.71
DANN	Benign	0.37
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs8137446; hg19: chr22-37347959;