rs6034368

Variant summary

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

The XM_011529286.3(SIRPG):​c.-27+8720G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,060 control chromosomes in the GnomAD database, including 5,276 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 ( 5276 hom., cov: 32)

Consequence

SIRPG
XM_011529286.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.379
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
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+8720G>A 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.461-6415G>A intron_variant 6

Frequencies

GnomAD3 genomes
AF:
0.245
AC:
37196
AN:
151942
Hom.:
5274
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.152
Gnomad AMI
AF:
0.139
Gnomad AMR
AF:
0.253
Gnomad ASJ
AF:
0.321
Gnomad EAS
AF:
0.587
Gnomad SAS
AF:
0.461
Gnomad FIN
AF:
0.281
Gnomad MID
AF:
0.383
Gnomad NFE
AF:
0.248
Gnomad OTH
AF:
0.279
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.245
AC:
37209
AN:
152060
Hom.:
5276
Cov.:
32
AF XY:
0.252
AC XY:
18753
AN XY:
74340
show subpopulations
Gnomad4 AFR
AF:
0.152
Gnomad4 AMR
AF:
0.253
Gnomad4 ASJ
AF:
0.321
Gnomad4 EAS
AF:
0.586
Gnomad4 SAS
AF:
0.460
Gnomad4 FIN
AF:
0.281
Gnomad4 NFE
AF:
0.249
Gnomad4 OTH
AF:
0.283
Alfa
AF:
0.261
Hom.:
2710
Bravo
AF:
0.235
Asia WGS
AF:
0.514
AC:
1788
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
6.0
DANN
Benign
0.36

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: rs6034368; hg19: chr20-1658258; API