rs7186310
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004594.3(SLC9A5):c.*400A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 205,502 control chromosomes in the GnomAD database, including 10,434 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.26 ( 9596 hom., cov: 32)
Exomes 𝑓: 0.12 ( 838 hom. )
Consequence
SLC9A5
NM_004594.3 3_prime_UTR
NM_004594.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0730
Genes affected
SLC9A5 (HGNC:11078): (solute carrier family 9 member A5) 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 be integral component of membrane. Predicted to be active in plasma membrane. Implicated in end stage renal disease. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC9A5 | NM_004594.3 | c.*400A>C | 3_prime_UTR_variant | 16/16 | ENST00000299798.16 | ||
LOC124903701 | XR_007065092.1 | n.462-5499T>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC9A5 | ENST00000299798.16 | c.*400A>C | 3_prime_UTR_variant | 16/16 | 1 | NM_004594.3 | P1 | ||
SLC9A5 | ENST00000563723.5 | n.3410A>C | non_coding_transcript_exon_variant | 15/15 | 1 | ||||
SLC9A5 | ENST00000564704.5 | n.4037A>C | non_coding_transcript_exon_variant | 16/16 | 1 | ||||
SLC9A5 | ENST00000564812.5 | c.*2353A>C | 3_prime_UTR_variant, NMD_transcript_variant | 15/15 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.262 AC: 39807AN: 151960Hom.: 9555 Cov.: 32
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GnomAD4 exome AF: 0.124 AC: 6627AN: 53424Hom.: 838 Cov.: 0 AF XY: 0.124 AC XY: 3452AN XY: 27842
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GnomAD4 genome ? AF: 0.262 AC: 39906AN: 152078Hom.: 9596 Cov.: 32 AF XY: 0.259 AC XY: 19293AN XY: 74364
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at