chr3-36504411-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_003149.3(STAC):c.785A>G(p.Asn262Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00475 in 1,613,536 control chromosomes in the GnomAD database, including 254 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Genomes: 𝑓 0.024 ( 129 hom., cov: 32)
Exomes 𝑓: 0.0028 ( 125 hom. )
Consequence
STAC
NM_003149.3 missense
NM_003149.3 missense
Scores
7
11
Clinical Significance
Conservation
PhyloP100: 5.66
Genes affected
STAC (HGNC:11353): (SH3 and cysteine rich domain) Predicted to enable transmembrane transporter binding activity. Predicted to be involved in positive regulation of protein localization to plasma membrane; positive regulation of voltage-gated calcium channel activity; and skeletal muscle contraction. Predicted to act upstream of or within cellular response to heat; muscle contraction; and regulation of voltage-gated calcium channel activity. Predicted to be located in T-tubule. Predicted to be extrinsic component of cytoplasmic side of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0021566153).
BP6
?
Variant 3-36504411-A-G is Benign according to our data. Variant chr3-36504411-A-G is described in ClinVar as [Benign]. Clinvar id is 783216.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0782 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STAC | NM_003149.3 | c.785A>G | p.Asn262Ser | missense_variant | 7/11 | ENST00000273183.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STAC | ENST00000273183.8 | c.785A>G | p.Asn262Ser | missense_variant | 7/11 | 1 | NM_003149.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0238 AC: 3620AN: 152166Hom.: 128 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00700 AC: 1757AN: 250826Hom.: 60 AF XY: 0.00523 AC XY: 709AN XY: 135544
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GnomAD4 exome AF: 0.00276 AC: 4030AN: 1461252Hom.: 125 Cov.: 30 AF XY: 0.00247 AC XY: 1797AN XY: 726930
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GnomAD4 genome ? AF: 0.0238 AC: 3630AN: 152284Hom.: 129 Cov.: 32 AF XY: 0.0232 AC XY: 1725AN XY: 74464
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ESP6500AA
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323
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ExAC
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1005
Asia WGS
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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 | Mar 29, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T;T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.;.
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Benign
T;T;T
Sift4G
Benign
T;T;T
Polyphen
D;D;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at