rs9745376
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The ENST00000543963.5(MSLNL):c.1833C>T(p.Asn611=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0203 in 529,760 control chromosomes in the GnomAD database, including 815 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 0.051 ( 638 hom., cov: 34)
Exomes 𝑓: 0.0077 ( 177 hom. )
Consequence
MSLNL
ENST00000543963.5 synonymous
ENST00000543963.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.833
Genes affected
MSLNL (HGNC:14170): (mesothelin like) Predicted to be involved in cell-matrix adhesion. Predicted to be located in membrane. Predicted to be integral component of membrane. Predicted to be active in cell surface. [provided by Alliance of Genome Resources, Apr 2022]
MIR662 (HGNC:32918): (microRNA 662) 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 Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP7
?
Synonymous conserved (PhyloP=-0.833 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MIR662 | NR_030384.1 | n.67G>A | non_coding_transcript_exon_variant | 1/1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MSLNL | ENST00000543963.5 | c.1833C>T | p.Asn611= | synonymous_variant | 14/15 | 5 | P1 | ||
MIR662 | ENST00000384847.1 | n.67G>A | mature_miRNA_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.0513 AC: 7800AN: 152088Hom.: 631 Cov.: 34
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GnomAD3 exomes AF: 0.0141 AC: 3316AN: 234604Hom.: 212 AF XY: 0.0103 AC XY: 1328AN XY: 128506
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GnomAD4 exome AF: 0.00774 AC: 2924AN: 377556Hom.: 177 Cov.: 0 AF XY: 0.00598 AC XY: 1287AN XY: 215072
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GnomAD4 genome ? AF: 0.0515 AC: 7836AN: 152204Hom.: 638 Cov.: 34 AF XY: 0.0499 AC XY: 3715AN XY: 74402
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at