rs10098474
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000562143.1(MSRA-DT):n.148G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 156,812 control chromosomes in the GnomAD database, including 35,440 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 0.65 ( 34115 hom., cov: 33)
Exomes 𝑓: 0.75 ( 1325 hom. )
Consequence
MSRA-DT
ENST00000562143.1 non_coding_transcript_exon
ENST00000562143.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.841
Genes affected
MSRA-DT (HGNC:55400): (MSRA divergent transcript)
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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=-0.78).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MSRA-DT | ENST00000562143.1 | n.148G>A | non_coding_transcript_exon_variant | 1/1 | |||||
ENST00000659604.1 | n.116+819G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.655 AC: 99529AN: 152054Hom.: 34135 Cov.: 33
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GnomAD4 exome AF: 0.751 AC: 3485AN: 4640Hom.: 1325 Cov.: 0 AF XY: 0.754 AC XY: 1658AN XY: 2198
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GnomAD4 genome ? AF: 0.654 AC: 99517AN: 152172Hom.: 34115 Cov.: 33 AF XY: 0.655 AC XY: 48710AN XY: 74388
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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