17-74748444-A-T
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000585285.1(SLC9A3R1-AS1):n.340+129T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000066 in 151,596 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SLC9A3R1-AS1
ENST00000585285.1 intron
ENST00000585285.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.761
Genes affected
SLC9A3R1-AS1 (HGNC:55322): (SLC9A3R1 antisense RNA 1)
NHERF1 (HGNC:11075): (NHERF family PDZ scaffold protein 1) This gene encodes a sodium/hydrogen exchanger regulatory cofactor. The protein interacts with and regulates various proteins including the cystic fibrosis transmembrane conductance regulator and G-protein coupled receptors such as the beta2-adrenergic receptor and the parathyroid hormone 1 receptor. The protein also interacts with proteins that function as linkers between integral membrane and cytoskeletal proteins. The protein localizes to actin-rich structures including membrane ruffles, microvilli, and filopodia. Mutations in this gene result in hypophosphatemic nephrolithiasis/osteoporosis type 2, and loss of heterozygosity of this gene is implicated in breast cancer.[provided by RefSeq, Sep 2009]
MIR3615 (HGNC:38905): (microRNA 3615) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC9A3R1-AS1 | NR_187307.1 | n.1160+129T>A | intron_variant | Intron 2 of 2 | ||||
NHERF1 | NM_004252.5 | c.-403A>T | upstream_gene_variant | ENST00000262613.10 | NP_004243.1 | |||
MIR3615 | NR_037409.1 | n.-169A>T | upstream_gene_variant | |||||
MIR3615 | unassigned_transcript_3091 | n.-219A>T | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC9A3R1-AS1 | ENST00000585285.1 | n.340+129T>A | intron_variant | Intron 1 of 1 | 3 | |||||
NHERF1 | ENST00000262613.10 | c.-403A>T | upstream_gene_variant | 1 | NM_004252.5 | ENSP00000262613.5 | ||||
NHERF1 | ENST00000583369.5 | c.-403A>T | upstream_gene_variant | 3 | ENSP00000464321.1 | |||||
MIR3615 | ENST00000581999.1 | n.-169A>T | upstream_gene_variant | 6 |
Frequencies
GnomAD3 genomes AF: 0.00000660 AC: 1AN: 151488Hom.: 0 Cov.: 32
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 4590Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 2360
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GnomAD4 genome AF: 0.00000660 AC: 1AN: 151596Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74130
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ClinVar
Not reported inComputational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at