20-1682353-G-T

Position:

• chr20-1682353-G-T

Variant summary

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

The XM_011529286.3(SIRPG):​c.-27+3979C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.808 in 152,132 control chromosomes in the GnomAD database, including 49,911 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 0.81 (49911 hom., cov: 32)
• Consequence: SIRPG XM_011529286.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.926

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]

SIRPB3P (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SIRPG	XM_011529286.3	c.-27+3979C>A		intron_variant			XP_011527588.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SIRPB3P	ENST00000340424.4	n.461-11156C>A		intron_variant		6

Frequencies

GnomAD3 genomes AF: 0.808 AC: 122857 AN: 152014 Hom.: 49891 Cov.: 32

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.847

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.901

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.830

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.808 AC: 122932 AN: 152132 Hom.: 49911 Cov.: 32 AF XY: 0.809 AC XY: 60145 AN XY: 74380

Gnomad4 AFR AF: 0.733

Gnomad4 AMR AF: 0.847

Gnomad4 ASJ AF: 0.791

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.900

Gnomad4 FIN AF: 0.768

Gnomad4 NFE AF: 0.830

Gnomad4 OTH AF: 0.810

Alfa AF: 0.825 Hom.: 68382

Bravo AF: 0.811

Asia WGS AF: 0.940 AC: 3267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.81
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs202548; hg19: chr20-1662999;