4-25655721-CGGCAGGTAGGCAGTGCCCCGGCGGCGGCTGCGGCAGGCGGTCCTGGAATGTGCGAGGGGCGTGATGACAGCGGCCAGCCTCTTTGCGCAACACCTTCGCCATATATACCCGGGGCGCTGCGCTCCACCTGGCCGCCGCCTCCAGCCCAGCACCTGCGGAGGGAGCGCTGGTGAGTACCGCCGCCGG-C
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The 4-25655721-CGGCAGGTAGGCAGTGCCCCGGCGGCGGCTGCGGCAGGCGGTCCTGGAATGTGCGAGGGGCGTGATGACAGCGGCCAGCCTCTTTGCGCAACACCTTCGCCATATATACCCGGGGCGCTGCGCTCCACCTGGCCGCCGCCTCCAGCCCAGCACCTGCGGAGGGAGCGCTGGTGAGTACCGCCGCCGG-C variant causes a splice donor, splice donor 5th base, 5 prime UTR, intron change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Consequence
NM_006424.3 splice_donor, splice_donor_5th_base, 5_prime_UTR, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC34A2 | NM_006424.3 | splice_donor_variant, splice_donor_5th_base_variant, 5_prime_UTR_variant, intron_variant | 1/13 | ENST00000382051.8 | |||
SLC34A2 | NM_001177998.2 | splice_donor_variant, splice_donor_5th_base_variant, 5_prime_UTR_variant, intron_variant | 1/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC34A2 | ENST00000382051.8 | splice_donor_variant, splice_donor_5th_base_variant, 5_prime_UTR_variant, intron_variant | 1/13 | 1 | NM_006424.3 | P4 | |||
SLC34A2 | ENST00000504570.5 | splice_donor_variant, splice_donor_5th_base_variant, 5_prime_UTR_variant, intron_variant | 1/13 | 1 | A2 | ||||
SLC34A2 | ENST00000513204.5 | c.-4+371_-4+556del | intron_variant | 4 | |||||
SLC34A2 | ENST00000645788.1 | c.-3-6770_-3-6585del | intron_variant | A2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
PULMONARY ALVEOLAR MICROLITHIASIS Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 01, 2006 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.