chr20-1562308-G-C

Variant names:

• chr20-1562308-G-C
• rs2253429
• NM_006065.5:c.*3192C>G

Variant summary

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

The NM_006065.5(SIRPB1):​c.*3192C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 151,900 control chromosomes in the GnomAD database, including 11,413 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 0.36 (11413 hom., cov: 32)
• Consequence: SIRPB1 NM_006065.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.328
• Publications: 6 publications found

Genes affected

SIRPB1 (HGNC:15928): (signal regulatory protein beta 1) The protein encoded by this gene is a member of the signal-regulatory-protein (SIRP) family, and also belongs to the immunoglobulin superfamily. SIRP family members are receptor-type transmembrane glycoproteins known to be involved in the negative regulation of receptor tyrosine kinase-coupled signaling processes. This protein was found to interact with TYROBP/DAP12, a protein bearing immunoreceptor tyrosine-based activation motifs. This protein was also reported to participate in the recruitment of tyrosine kinase SYK. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2009]

ENSG00000260861 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SIRPB1	NM_006065.5	c.*3192C>G		3_prime_UTR_variant	Exon 6 of 6	ENST00000381605.9	NP_006056.2
SIRPB1	NM_001083910.4	c.*3192C>G		3_prime_UTR_variant	Exon 4 of 4		NP_001077379.1
SIRPB1	NM_001330639.2	c.*3192C>G		3_prime_UTR_variant	Exon 4 of 4		NP_001317568.1
SIRPB1	XM_005260641.4	c.*3192C>G		3_prime_UTR_variant	Exon 6 of 6		XP_005260698.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SIRPB1	ENST00000381605.9	c.*3192C>G		3_prime_UTR_variant	Exon 6 of 6	1	NM_006065.5	ENSP00000371018.5
ENSG00000260861	ENST00000564763.1	c.434-10259C>G		intron_variant	Intron 2 of 2	4		ENSP00000457944.1
ENSG00000260861	ENST00000567028.5	c.431-10270C>G		intron_variant	Intron 2 of 2	4		ENSP00000454437.1
ENSG00000260861	ENST00000566961.2	c.206-4564C>G		intron_variant	Intron 1 of 2	3		ENSP00000457551.2

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54461 AN: 151782 Hom.: 11416 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.0204

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.359 AC: 54480 AN: 151900 Hom.: 11413 Cov.: 32 AF XY: 0.355 AC XY: 26349 AN XY: 74226

African (AFR) AF: 0.190 AC: 7873 AN: 41436

American (AMR) AF: 0.286 AC: 4367 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1504 AN: 3462

East Asian (EAS) AF: 0.0205 AC: 106 AN: 5180

South Asian (SAS) AF: 0.317 AC: 1530 AN: 4820

European-Finnish (FIN) AF: 0.537 AC: 5649 AN: 10528

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32154 AN: 67896

Other (OTH) AF: 0.373 AC: 787 AN: 2112

Alfa AF: 0.296 Hom.: 891

Bravo AF: 0.331

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.66
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs2253429; hg19: chr20-1542954;