12-65621787-C-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_120431.1(MSRB3-AS1):n.334+20252G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 152,014 control chromosomes in the GnomAD database, including 31,250 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 0.61 ( 31250 hom., cov: 32)
Consequence
MSRB3-AS1
NR_120431.1 intron, non_coding_transcript
NR_120431.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.845
Genes affected
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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=-0.81).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MSRB3-AS1 | NR_120431.1 | n.334+20252G>T | intron_variant, non_coding_transcript_variant | ||||
MSRB3-AS1 | NR_120432.1 | n.408+4825G>T | intron_variant, non_coding_transcript_variant | ||||
MSRB3-AS1 | NR_120433.1 | n.335-8510G>T | intron_variant, non_coding_transcript_variant | ||||
MSRB3-AS1 | NR_120434.1 | n.335-8510G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MSRB3-AS1 | ENST00000537250.5 | n.160+20252G>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.607 AC: 92249AN: 151896Hom.: 31245 Cov.: 32
GnomAD3 genomes
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92249
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32
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GnomAD4 genome ? AF: 0.607 AC: 92273AN: 152014Hom.: 31250 Cov.: 32 AF XY: 0.611 AC XY: 45407AN XY: 74306
GnomAD4 genome
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32
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45407
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74306
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2173
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3478
ClinVar
Not reported inComputational 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