rs1638421
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_025015.3(HSPA12A):c.40+13226G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000592 in 152,002 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000059 ( 0 hom., cov: 32)
Consequence
HSPA12A
NM_025015.3 intron
NM_025015.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.860
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BS2
?
High AC in GnomAd4 at 9 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HSPA12A | NM_025015.3 | c.40+13226G>T | intron_variant | ENST00000369209.8 | |||
HSPA12A | NM_001330164.2 | c.92-21919G>T | intron_variant | ||||
HSPA12A | XM_005269673.6 | c.89-21919G>T | intron_variant | ||||
HSPA12A | XM_011539579.3 | c.89-21919G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSPA12A | ENST00000369209.8 | c.40+13226G>T | intron_variant | 1 | NM_025015.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000592 AC: 9AN: 152002Hom.: 0 Cov.: 32
GnomAD3 genomes
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152002
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0000592 AC: 9AN: 152002Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74220
GnomAD4 genome
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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