rs7659335
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001352885.1(SMIM31):c.-25-1905T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 151,036 control chromosomes in the GnomAD database, including 18,200 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 0.48 ( 18200 hom., cov: 29)
Consequence
SMIM31
NM_001352885.1 intron
NM_001352885.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.283
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=-0.9).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMIM31 | NM_001352885.1 | c.-25-1905T>C | intron_variant | ENST00000507311.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMIM31 | ENST00000507311.1 | c.-25-1905T>C | intron_variant | 1 | NM_001352885.1 | P1 | |||
SMIM31 | ENST00000515485.5 | c.-25-1905T>C | intron_variant | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.478 AC: 72141AN: 150930Hom.: 18181 Cov.: 29
GnomAD3 genomes
?
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150930
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29
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.478 AC: 72169AN: 151036Hom.: 18200 Cov.: 29 AF XY: 0.474 AC XY: 34942AN XY: 73686
GnomAD4 genome
?
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72169
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151036
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29
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34942
AN XY:
73686
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Asia WGS
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1551
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3478
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