rs7041
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_000583.4(GC):c.1296T>G(p.Asp432Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 151994 control chromosomes in the gnomAD Genomes database, including 17953 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Genomes: 𝑓 0.45 ( 17953 hom., cov: 32)
Exomes 𝑓: 0.52 ( 36331 hom. )
Consequence
GC
NM_000583.4 missense
NM_000583.4 missense
Scores
18
Clinical Significance
Conservation
PhyloP100: -3.89
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=4.460173E-6).
BP6
?
Variant 4-71752617-A-C is Benign according to our data. Variant chr4-71752617-A-C is described in ClinVar as [Benign]. Clinvar id is 15987. Status of the report is no_assertion_criteria_provided, 0 stars.
BA1
?
GnomAd highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GC | NM_000583.4 | c.1296T>G | p.Asp432Glu | missense_variant | 11/13 | ENST00000273951.13 | |
GC | NM_001204307.1 | c.1353T>G | p.Asp451Glu | missense_variant | 12/14 | ||
GC | NM_001204306.1 | c.1296T>G | p.Asp432Glu | missense_variant | 12/14 | ||
GC | XM_006714177.3 | c.1262+1794T>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GC | ENST00000273951.13 | c.1296T>G | p.Asp432Glu | missense_variant | 11/13 | 1 | NM_000583.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.449 AC: 68273AN: 151994Hom.: 17953 Cov.: 32
GnomAD3 genomes
AF:
AC:
68273
AN:
151994
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: 0.522 AC: 131047AN: 251206Hom.: 36331 AF XY: 0.531 AC XY: 72119AN XY: 135784
GnomAD3 exomes
AF:
AC:
131047
AN:
251206
Hom.:
AF XY:
AC XY:
72119
AN XY:
135784
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: 0.545 AC: 796152AN: 1459866Hom.: 222353 AF XY: 0.547 AC XY: 397490AN XY: 726388
GnomAD4 exome
AF:
AC:
796152
AN:
1459866
Hom.:
AF XY:
AC XY:
397490
AN XY:
726388
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:
Alfa
AF:
Hom.:
Bravo
AF:
TwinsUK
AF:
AC:
2073
ALSPAC
AF:
AC:
2140
ESP6500AA
AF:
AC:
765
ESP6500EA
AF:
AC:
4808
ExAC
AF:
AC:
62622
Asia WGS
AF:
AC:
1434
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
GC1/GC2 POLYMORPHISM Benign:1
Benign, no assertion criteria provided | literature only | OMIM | Jun 01, 1992 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;.;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.;.
MutationTaster
Benign
P;P;P
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
0.0
.;.;B
Vest4
MutPred
Gain of glycosylation at T434 (P = 0.0279);.;Gain of glycosylation at T434 (P = 0.0279);
MPC
0.048
ClinPred
T
GERP RS
Varity_R
gMVP
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