20-1487272-T-C

Variant names:

• chr20-1487272-T-C
• rs6079325
• NM_001122962.2:c.85+4003A>G

Variant summary

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

The NM_001122962.2(SIRPB2):​c.85+4003A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 151,924 control chromosomes in the GnomAD database, including 17,100 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 0.44 (17100 hom., cov: 32)
• Consequence: SIRPB2 NM_001122962.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.453
• Publications: 16 publications found

Genes affected

SIRPB2 (HGNC:16247): (signal regulatory protein beta 2) Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001122962.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SIRPB2	NM_001122962.2	MANE Select	c.85+4003A>G		intron	N/A	NP_001116434.1	Q5JXA9-1
	SIRPB2	NM_001134836.2		c.85+4003A>G		intron	N/A	NP_001128308.1	Q5JXA9-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SIRPB2	ENST00000359801.8	TSL:2 MANE Select	c.85+4003A>G		intron	N/A	ENSP00000352849.3	Q5JXA9-1
	SIRPB2	ENST00000381630.2	TSL:1	n.109+4003A>G		intron	N/A
	SIRPB2	ENST00000444444.2	TSL:2	c.85+4003A>G		intron	N/A	ENSP00000402438.1	Q5JXA9-3

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67504 AN: 151806 Hom.: 17057 Cov.: 32

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.445 AC: 67595 AN: 151924 Hom.: 17100 Cov.: 32 AF XY: 0.446 AC XY: 33138 AN XY: 74262

African (AFR) AF: 0.655 AC: 27157 AN: 41438

American (AMR) AF: 0.506 AC: 7719 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1350 AN: 3462

East Asian (EAS) AF: 0.748 AC: 3870 AN: 5172

South Asian (SAS) AF: 0.499 AC: 2404 AN: 4820

European-Finnish (FIN) AF: 0.242 AC: 2548 AN: 10534

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21295 AN: 67924

Other (OTH) AF: 0.444 AC: 937 AN: 2108

Alfa AF: 0.360 Hom.: 14409

Bravo AF: 0.477

Asia WGS AF: 0.616 AC: 2132 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.47
PhyloP100		-0.45
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs6079325; hg19: chr20-1467917;