rs78958330
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The ENST00000398120.6(SLC9B1P2):n.449-95A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 0.000040 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00049 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SLC9B1P2
ENST00000398120.6 intron, non_coding_transcript
ENST00000398120.6 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.902
Genes affected
SLC9B1P2 (HGNC:37493): (solute carrier family 9 member B1 pseudogene 2)
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC9B1P2 | ENST00000398120.6 | n.449-95A>G | intron_variant, non_coding_transcript_variant | ||||||
ENST00000606405.1 | n.168-95A>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 6AN: 148530Hom.: 0 Cov.: 33 FAILED QC
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33
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000490 AC: 158AN: 322544Hom.: 0 AF XY: 0.000410 AC XY: 72AN XY: 175552
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.0000404 AC: 6AN: 148630Hom.: 0 Cov.: 33 AF XY: 0.0000690 AC XY: 5AN XY: 72476
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Data not reliable, filtered out with message: AS_VQSR
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at