20-1562420-G-T

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_006065.5(SIRPB1):​c.*3080C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

Alfa AF: 0.00 Hom.: 4947

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.2
DANN	Benign	0.74
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;