rs4954265
Variant names:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001378107.1(R3HDM1):c.-250+35022A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 749,052 control chromosomes in the GnomAD database, including 13,156 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 0.26 ( 8817 hom., cov: 32)
Exomes 𝑓: 0.079 ( 4339 hom. )
Consequence
R3HDM1
NM_001378107.1 intron
NM_001378107.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.435
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=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
R3HDM1 | NM_001378107.1 | c.-250+35022A>G | intron_variant | Intron 1 of 26 | ENST00000683871.1 | NP_001365036.1 | ||
R3HDM1 | NM_001354200.2 | c.-250+35022A>G | intron_variant | Intron 1 of 25 | NP_001341129.1 | |||
R3HDM1 | NM_015361.4 | c.-250+35022A>G | intron_variant | Intron 1 of 25 | NP_056176.2 | |||
R3HDM1 | NM_001282799.2 | c.-250+35022A>G | intron_variant | Intron 1 of 22 | NP_001269728.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
R3HDM1 | ENST00000683871.1 | c.-250+35022A>G | intron_variant | Intron 1 of 26 | NM_001378107.1 | ENSP00000506980.1 |
Frequencies
GnomAD3 genomes AF: 0.256 AC: 38907AN: 151958Hom.: 8788 Cov.: 32
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GnomAD4 exome AF: 0.0789 AC: 47125AN: 596976Hom.: 4339 Cov.: 8 AF XY: 0.0788 AC XY: 22024AN XY: 279482
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GnomAD4 genome AF: 0.256 AC: 38987AN: 152076Hom.: 8817 Cov.: 32 AF XY: 0.257 AC XY: 19116AN XY: 74356
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at