rs3848788

Variant names:

• chr20-1562420-G-A
• rs3848788
• NM_006065.5:c.*3080C>T

Your query was ambiguous. Multiple possible variants found:

• chr20-1562420-G-A
• chr20-1562420-G-T

Variant summary

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

The NM_006065.5(SIRPB1):​c.*3080C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 151,744 control chromosomes in the GnomAD database, including 16,382 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 0.43 (16382 hom., cov: 30)
• Consequence: SIRPB1 NM_006065.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730
• Publications: 13 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SIRPB1	NM_006065.5	c.*3080C>T		3_prime_UTR_variant	Exon 6 of 6	ENST00000381605.9	NP_006056.2
SIRPB1	NM_001083910.4	c.*3080C>T		3_prime_UTR_variant	Exon 4 of 4		NP_001077379.1
SIRPB1	NM_001330639.2	c.*3080C>T		3_prime_UTR_variant	Exon 4 of 4		NP_001317568.1
SIRPB1	XM_005260641.4	c.*3080C>T		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.*3080C>T		3_prime_UTR_variant	Exon 6 of 6	1	NM_006065.5	ENSP00000371018.5
ENSG00000260861	ENST00000564763.1	c.434-10371C>T		intron_variant	Intron 2 of 2	4		ENSP00000457944.1
ENSG00000260861	ENST00000567028.5	c.431-10382C>T		intron_variant	Intron 2 of 2	4		ENSP00000454437.1
ENSG00000260861	ENST00000566961.2	c.206-4676C>T		intron_variant	Intron 1 of 2	3		ENSP00000457551.2

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65592 AN: 151630 Hom.: 16352 Cov.: 30

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.780

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.433 AC: 65671 AN: 151744 Hom.: 16382 Cov.: 30 AF XY: 0.434 AC XY: 32195 AN XY: 74168

African (AFR) AF: 0.660 AC: 27275 AN: 41308

American (AMR) AF: 0.414 AC: 6309 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1372 AN: 3468

East Asian (EAS) AF: 0.780 AC: 4032 AN: 5166

South Asian (SAS) AF: 0.467 AC: 2246 AN: 4810

European-Finnish (FIN) AF: 0.271 AC: 2849 AN: 10504

Middle Eastern (MID) AF: 0.459 AC: 133 AN: 290

European-Non Finnish (NFE) AF: 0.298 AC: 20265 AN: 67928

Other (OTH) AF: 0.427 AC: 901 AN: 2112

Alfa AF: 0.338 Hom.: 4947

Bravo AF: 0.455

Asia WGS AF: 0.606 AC: 2104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.4
DANN	Benign	0.78
PhyloP100		0.073

Splicing

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

Other links and lift over

dbSNP: rs3848788; hg19: chr20-1543066;