rs2253429

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr20-1562308-G-A
• chr20-1562308-G-C

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.*3192C>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 0.0000658 in 152,002 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000066 (0 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: 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=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SIRPB1	NM_006065.5	c.*3192C>T		3_prime_UTR_variant	Exon 6 of 6	ENST00000381605.9	NP_006056.2
SIRPB1	NM_001083910.4	c.*3192C>T		3_prime_UTR_variant	Exon 4 of 4		NP_001077379.1
SIRPB1	NM_001330639.2	c.*3192C>T		3_prime_UTR_variant	Exon 4 of 4		NP_001317568.1
SIRPB1	XM_005260641.4	c.*3192C>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.*3192C>T		3_prime_UTR_variant	Exon 6 of 6	1	NM_006065.5	ENSP00000371018.5
ENSG00000260861	ENST00000564763.1	c.434-10259C>T		intron_variant	Intron 2 of 2	4		ENSP00000457944.1
ENSG00000260861	ENST00000567028.5	c.431-10270C>T		intron_variant	Intron 2 of 2	4		ENSP00000454437.1
ENSG00000260861	ENST00000566961.2	c.206-4564C>T		intron_variant	Intron 1 of 2	3		ENSP00000457551.2

Frequencies

GnomAD3 genomes AF: 0.0000658 AC: 10 AN: 151884 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000484

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000883

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.0000658 AC: 10 AN: 152002 Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5 AN XY: 74296

African (AFR) AF: 0.0000482 AC: 2 AN: 41466

American (AMR) AF: 0.00 AC: 0 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3462

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.000415 AC: 2 AN: 4824

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10550

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000883 AC: 6 AN: 67932

Other (OTH) AF: 0.00 AC: 0 AN: 2114

Alfa AF: 0.0000866 Hom.: 891

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.44
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;