chr11-106939832-A-G
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_000855.3(GUCY1A2):c.834T>C(p.Ser278=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0023 in 1,613,832 control chromosomes in the GnomAD database, including 117 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0031 ( 15 hom., cov: 32)
Exomes 𝑓: 0.0022 ( 102 hom. )
Consequence
GUCY1A2
NM_000855.3 synonymous
NM_000855.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.719
Genes affected
GUCY1A2 (HGNC:4684): (guanylate cyclase 1 soluble subunit alpha 2) Soluble guanylate cyclases are heterodimeric proteins that catalyze the conversion of GTP to 3',5'-cyclic GMP and pyrophosphate. The protein encoded by this gene is an alpha subunit of this complex and it interacts with a beta subunit to form the guanylate cyclase enzyme, which is activated by nitric oxide. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]
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=-0.85).
BP6
?
Variant 11-106939832-A-G is Benign according to our data. Variant chr11-106939832-A-G is described in ClinVar as [Benign]. Clinvar id is 770221.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.719 with no splicing effect.
BA1
?
GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0575 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GUCY1A2 | NM_000855.3 | c.834T>C | p.Ser278= | synonymous_variant | 4/8 | ENST00000526355.7 | |
GUCY1A2 | NM_001256424.2 | c.834T>C | p.Ser278= | synonymous_variant | 4/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GUCY1A2 | ENST00000526355.7 | c.834T>C | p.Ser278= | synonymous_variant | 4/8 | 1 | NM_000855.3 | P1 | |
GUCY1A2 | ENST00000282249.6 | c.834T>C | p.Ser278= | synonymous_variant | 4/9 | 1 | |||
GUCY1A2 | ENST00000347596.2 | c.834T>C | p.Ser278= | synonymous_variant | 4/9 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00306 AC: 466AN: 152204Hom.: 14 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
466
AN:
152204
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00935 AC: 2351AN: 251404Hom.: 81 AF XY: 0.00671 AC XY: 912AN XY: 135878
GnomAD3 exomes
AF:
AC:
2351
AN:
251404
Hom.:
AF XY:
AC XY:
912
AN XY:
135878
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00222 AC: 3245AN: 1461510Hom.: 102 Cov.: 31 AF XY: 0.00185 AC XY: 1344AN XY: 727074
GnomAD4 exome
AF:
AC:
3245
AN:
1461510
Hom.:
Cov.:
31
AF XY:
AC XY:
1344
AN XY:
727074
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.00307 AC: 468AN: 152322Hom.: 15 Cov.: 32 AF XY: 0.00320 AC XY: 238AN XY: 74484
GnomAD4 genome
?
AF:
AC:
468
AN:
152322
Hom.:
Cov.:
32
AF XY:
AC XY:
238
AN XY:
74484
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
11
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 submitter | clinical testing | Invitae | Feb 08, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at