chr20-1678815-G-A

Variant names:

• chr20-1678815-G-A
• rs1438106
• ENST00000340424.4:n.461-7618C>T

Variant summary

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

The ENST00000340424.4(SIRPB3P):​n.461-7618C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 152,044 control chromosomes in the GnomAD database, including 5,208 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 0.24 (5208 hom., cov: 32)
• Consequence: SIRPB3P ENST00000340424.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.224
• Publications: 1 publications found

Genes affected

SIRPB3P (HGNC:49209): (signal regulatory protein beta 3, pseudogene)

ENSG00000296776 (HGNC:):

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]

SIRPG Gene-Disease associations (from GenCC):

• male infertility with azoospermia or oligozoospermia due to single gene mutation

  Inheritance: AR Classification: LIMITED Submitted by: King Faisal Specialist Hospital and Research Center

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000340424.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SIRPB3P	ENST00000340424.4	TSL:6	n.461-7618C>T		intron	N/A
	ENSG00000296776	ENST00000741926.1		n.135+7517C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36970 AN: 151926 Hom.: 5206 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.243 AC: 36983 AN: 152044 Hom.: 5208 Cov.: 32 AF XY: 0.251 AC XY: 18615 AN XY: 74306

African (AFR) AF: 0.151 AC: 6276 AN: 41486

American (AMR) AF: 0.246 AC: 3754 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1112 AN: 3470

East Asian (EAS) AF: 0.586 AC: 3026 AN: 5164

South Asian (SAS) AF: 0.461 AC: 2226 AN: 4828

European-Finnish (FIN) AF: 0.280 AC: 2955 AN: 10556

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16800 AN: 67968

Other (OTH) AF: 0.282 AC: 594 AN: 2110

Alfa AF: 0.252 Hom.: 890

Bravo AF: 0.233

Asia WGS AF: 0.515 AC: 1791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.7
DANN	Benign	0.94
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs1438106; hg19: chr20-1659461;