rs1048055

chr20-1629416-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018556.4(SIRPG):c.*223T>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 0.693 in 152,042 control chromosomes in the GnomAD database, including 36,828 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 0.69 (36789 hom., cov: 30)
  • Exomes 𝑓: 0.78 (39 hom.)
• Consequence: SIRPG NM_018556.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.788

Genes affected

SIRPG (HGNC:15757): (signal regulatory protein gamma) 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. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.846 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SIRPG	NM_018556.4	c.*223T>G		3_prime_UTR_variant	6/6	ENST00000303415.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SIRPG	ENST00000303415.7	c.*223T>G		3_prime_UTR_variant	6/6	1	NM_018556.4	P2

Frequencies

GnomAD3 genomes AF: 0.693 AC: 105205 AN: 151804 Hom.: 36765 Cov.: 30

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.753

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.822

Gnomad SAS AF: 0.869

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.707

GnomAD4 exome AF: 0.775 AC: 93 AN: 120 Hom.: 39 Cov.: 0 AF XY: 0.787 AC XY: 74 AN XY: 94

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 1.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.774

Gnomad4 OTH exome AF: 0.800

GnomAD4 genome AF: 0.693 AC: 105286 AN: 151922 Hom.: 36789 Cov.: 30 AF XY: 0.701 AC XY: 52055 AN XY: 74254

Gnomad4 AFR AF: 0.643

Gnomad4 AMR AF: 0.753

Gnomad4 ASJ AF: 0.779

Gnomad4 EAS AF: 0.822

Gnomad4 SAS AF: 0.868

Gnomad4 FIN AF: 0.730

Gnomad4 NFE AF: 0.679

Gnomad4 OTH AF: 0.708

Alfa AF: 0.682 Hom.: 12712

Bravo AF: 0.686

Asia WGS AF: 0.811 AC: 2820 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.6
Dann	Benign	0.73

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

Publications

LitVar

Other links and lift over

dbSNP: rs1048055; hg19: chr20-1610062;