rs1438106

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The XM_011529286.3(SIRPG):​c.-27+7517C>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

SIRPG
XM_011529286.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.224
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SIRPGXM_011529286.3 linkuse as main transcriptc.-27+7517C>T intron_variant XP_011527588.1 Q9P1W8-2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SIRPB3PENST00000340424.4 linkuse as main transcriptn.461-7618C>T intron_variant 6

Frequencies

GnomAD3 genomes
AF:
0.243
AC:
36970
AN:
151926
Hom.:
5206
Cov.:
32
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.151
Gnomad4 AMR
AF:
0.246
Gnomad4 ASJ
AF:
0.320
Gnomad4 EAS
AF:
0.586
Gnomad4 SAS
AF:
0.461
Gnomad4 FIN
AF:
0.280
Gnomad4 NFE
AF:
0.247
Gnomad4 OTH
AF:
0.282
Alfa
AF:
0.255
Hom.:
879
Bravo
AF:
0.233
Asia WGS
AF:
0.515
AC:
1791
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1438106; hg19: chr20-1659461; API