chr6-32191414-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_001276501.2(GPSM3):​c.435G>A​(p.Gly145=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00481 in 1,593,600 control chromosomes in the GnomAD database, including 82 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0047 ( 10 hom., cov: 31)
Exomes 𝑓: 0.0048 ( 72 hom. )

Consequence

GPSM3
NM_001276501.2 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.889
Variant links:
Genes affected
GPSM3 (HGNC:13945): (G protein signaling modulator 3) Predicted to enable GTPase regulator activity. Predicted to be involved in positive regulation of inflammatory response. Predicted to act upstream of or within positive regulation of cytokine production involved in inflammatory response and positive regulation of leukocyte chemotaxis. Predicted to be located in cytoplasm and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BP6
Variant 6-32191414-C-T is Benign according to our data. Variant chr6-32191414-C-T is described in ClinVar as [Benign]. Clinvar id is 770360.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.889 with no splicing effect.
BS1
Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00481 (6938/1441414) while in subpopulation MID AF= 0.0165 (94/5698). AF 95% confidence interval is 0.0151. There are 72 homozygotes in gnomad4_exome. There are 3784 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 10 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GPSM3NM_001276501.2 linkuse as main transcriptc.435G>A p.Gly145= synonymous_variant 4/4 ENST00000375040.8
GPSM3NM_022107.3 linkuse as main transcriptc.435G>A p.Gly145= synonymous_variant 8/8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GPSM3ENST00000375040.8 linkuse as main transcriptc.435G>A p.Gly145= synonymous_variant 4/41 NM_001276501.2 P1

Frequencies

GnomAD3 genomes
AF:
0.00472
AC:
718
AN:
152068
Hom.:
10
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00135
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00812
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00987
Gnomad SAS
AF:
0.0158
Gnomad FIN
AF:
0.00424
Gnomad MID
AF:
0.0158
Gnomad NFE
AF:
0.00500
Gnomad OTH
AF:
0.0101
GnomAD3 exomes
AF:
0.00657
AC:
1543
AN:
234894
Hom.:
17
AF XY:
0.00707
AC XY:
905
AN XY:
127938
show subpopulations
Gnomad AFR exome
AF:
0.00116
Gnomad AMR exome
AF:
0.00744
Gnomad ASJ exome
AF:
0.000324
Gnomad EAS exome
AF:
0.00743
Gnomad SAS exome
AF:
0.0155
Gnomad FIN exome
AF:
0.00380
Gnomad NFE exome
AF:
0.00569
Gnomad OTH exome
AF:
0.00689
GnomAD4 exome
AF:
0.00481
AC:
6938
AN:
1441414
Hom.:
72
Cov.:
31
AF XY:
0.00528
AC XY:
3784
AN XY:
716870
show subpopulations
Gnomad4 AFR exome
AF:
0.00119
Gnomad4 AMR exome
AF:
0.00988
Gnomad4 ASJ exome
AF:
0.000197
Gnomad4 EAS exome
AF:
0.00432
Gnomad4 SAS exome
AF:
0.0158
Gnomad4 FIN exome
AF:
0.00361
Gnomad4 NFE exome
AF:
0.00378
Gnomad4 OTH exome
AF:
0.00944
GnomAD4 genome
AF:
0.00474
AC:
722
AN:
152186
Hom.:
10
Cov.:
31
AF XY:
0.00464
AC XY:
345
AN XY:
74406
show subpopulations
Gnomad4 AFR
AF:
0.00135
Gnomad4 AMR
AF:
0.00824
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00989
Gnomad4 SAS
AF:
0.0158
Gnomad4 FIN
AF:
0.00424
Gnomad4 NFE
AF:
0.00500
Gnomad4 OTH
AF:
0.0118
Alfa
AF:
0.00396
Hom.:
2
Bravo
AF:
0.00426
Asia WGS
AF:
0.0400
AC:
137
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpMay 25, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.50
CADD
Benign
6.3
DANN
Benign
0.83

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

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

Other links and lift over

dbSNP: rs145686781; hg19: chr6-32159191; COSMIC: COSV66683157; COSMIC: COSV66683157; API