rs1014286
Positions:
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_001011552.4(SLC9A4):c.2350G>A(p.Gly784Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.63 in 1,613,224 control chromosomes in the GnomAD database, including 321,379 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).
Frequency
Genomes: 𝑓 0.64 ( 31285 hom., cov: 31)
Exomes 𝑓: 0.63 ( 290094 hom. )
Consequence
SLC9A4
NM_001011552.4 missense
NM_001011552.4 missense
Scores
18
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.493
Genes affected
SLC9A4 (HGNC:11077): (solute carrier family 9 member A4) Predicted to enable potassium:proton antiporter activity and sodium:proton antiporter activity. Predicted to be involved in potassium ion transmembrane transport; regulation of intracellular pH; and sodium ion import across plasma membrane. Predicted to act upstream of or within epithelial cell development and gastric acid secretion. Predicted to be located in several cellular components, including apical plasma membrane; basolateral plasma membrane; and vacuolar membrane. Predicted to be integral component of membrane. Predicted to be active in 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 -13 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=2.7308365E-6).
BP6
?
Variant 2-102532641-G-A is Benign according to our data. Variant chr2-102532641-G-A is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC9A4 | NM_001011552.4 | c.2350G>A | p.Gly784Ser | missense_variant | 12/12 | ENST00000295269.5 | |
SLC9A4 | XM_011511158.2 | c.2263G>A | p.Gly755Ser | missense_variant | 12/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC9A4 | ENST00000295269.5 | c.2350G>A | p.Gly784Ser | missense_variant | 12/12 | 1 | NM_001011552.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.640 AC: 97211AN: 151890Hom.: 31244 Cov.: 31
GnomAD3 genomes
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GnomAD3 exomes AF: 0.634 AC: 158608AN: 250046Hom.: 50862 AF XY: 0.629 AC XY: 85034AN XY: 135122
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GnomAD4 exome AF: 0.629 AC: 918730AN: 1461218Hom.: 290094 Cov.: 64 AF XY: 0.627 AC XY: 455952AN XY: 726868
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GnomAD4 genome ? AF: 0.640 AC: 97308AN: 152006Hom.: 31285 Cov.: 31 AF XY: 0.642 AC XY: 47696AN XY: 74294
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
MutationTaster
Benign
P
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
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