ENST00000585285.1:n.340+100C>T
Variant names:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The ENST00000585285.1(SLC9A3R1-AS1):n.340+100C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0198 in 166,078 control chromosomes in the GnomAD database, including 43 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.020 ( 38 hom., cov: 34)
Exomes 𝑓: 0.019 ( 5 hom. )
Consequence
SLC9A3R1-AS1
ENST00000585285.1 intron
ENST00000585285.1 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.784
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
BP6
Variant 17-74748473-G-A is Benign according to our data. Variant chr17-74748473-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1316461.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0199 (3028/151912) while in subpopulation SAS AF= 0.0352 (170/4830). AF 95% confidence interval is 0.0309. There are 38 homozygotes in gnomad4. There are 1508 alleles in male gnomad4 subpopulation. Median coverage is 34. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 38 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC9A3R1-AS1 | NR_187307.1 | n.1160+100C>T | intron_variant | Intron 2 of 2 | ||||
NHERF1 | NM_004252.5 | c.-374G>A | upstream_gene_variant | ENST00000262613.10 | NP_004243.1 | |||
MIR3615 | NR_037409.1 | n.-140G>A | upstream_gene_variant | |||||
MIR3615 | unassigned_transcript_3091 | n.-190G>A | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC9A3R1-AS1 | ENST00000585285.1 | n.340+100C>T | intron_variant | Intron 1 of 1 | 3 | |||||
NHERF1 | ENST00000262613.10 | c.-374G>A | upstream_gene_variant | 1 | NM_004252.5 | ENSP00000262613.5 | ||||
NHERF1 | ENST00000583369.5 | c.-374G>A | upstream_gene_variant | 3 | ENSP00000464321.1 | |||||
MIR3615 | ENST00000581999.1 | n.-140G>A | upstream_gene_variant | 6 |
Frequencies
GnomAD3 genomes AF: 0.0199 AC: 3024AN: 151804Hom.: 38 Cov.: 34
GnomAD3 genomes
AF:
AC:
3024
AN:
151804
Hom.:
Cov.:
34
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:
GnomAD4 exome AF: 0.0188 AC: 267AN: 14166Hom.: 5 AF XY: 0.0221 AC XY: 158AN XY: 7160
GnomAD4 exome
AF:
AC:
267
AN:
14166
Hom.:
AF XY:
AC XY:
158
AN XY:
7160
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:
GnomAD4 genome AF: 0.0199 AC: 3028AN: 151912Hom.: 38 Cov.: 34 AF XY: 0.0203 AC XY: 1508AN XY: 74262
GnomAD4 genome
AF:
AC:
3028
AN:
151912
Hom.:
Cov.:
34
AF XY:
AC XY:
1508
AN XY:
74262
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Oct 07, 2019
GeneDx
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at