22-36921872-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_000395.3(CSF2RB):c.-172-164C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0537 in 152,300 control chromosomes in the GnomAD database, including 242 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.054 (242 hom., cov: 33)
• Consequence: CSF2RB NM_000395.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.538

Genes affected

CSF2RB (HGNC:2436): (colony stimulating factor 2 receptor subunit beta) The protein encoded by this gene is the common beta chain of the high affinity receptor for IL-3, IL-5 and CSF. Defects in this gene have been reported to be associated with protein alveolar proteinosis (PAP). [provided by RefSeq, Jul 2008]

LOC105373023 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 22-36921872-C-T is Benign according to our data. Variant chr22-36921872-C-T is described in ClinVar as [Benign]. Clinvar id is 1178164.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0945 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSF2RB	NM_000395.3	c.-172-164C>T		intron_variant		ENST00000403662.8
LOC105373023	XR_938230.2	n.195-2933G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSF2RB	ENST00000403662.8	c.-172-164C>T		intron_variant		5	NM_000395.3	P1

Frequencies

GnomAD3 genomes AF: 0.0537 AC: 8179 AN: 152182 Hom.: 241 Cov.: 33

Gnomad AFR AF: 0.0690

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0400

Gnomad ASJ AF: 0.0268

Gnomad EAS AF: 0.0418

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0518

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0465

Gnomad OTH AF: 0.0569

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

GnomAD4 genome AF: 0.0537 AC: 8186 AN: 152300 Hom.: 242 Cov.: 33 AF XY: 0.0541 AC XY: 4026 AN XY: 74466

Gnomad4 AFR AF: 0.0689

Gnomad4 AMR AF: 0.0399

Gnomad4 ASJ AF: 0.0268

Gnomad4 EAS AF: 0.0419

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.0518

Gnomad4 NFE AF: 0.0465

Gnomad4 OTH AF: 0.0572

Alfa AF: 0.0462 Hom.: 29

Bravo AF: 0.0524

Asia WGS AF: 0.0560 AC: 195 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 10, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	1.3
Dann	Benign	0.78

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs41280007; hg19: chr22-37317914;