8-22404629-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001128431.4(SLC39A14):c.-15-67G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 1,466,832 control chromosomes in the GnomAD database, including 37,682 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001128431.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC39A14 | ENST00000359741.10 | c.-15-67G>A | intron_variant | Intron 1 of 8 | 2 | NM_015359.6 | ENSP00000352779.5 | |||
SLC39A14 | ENST00000381237.6 | c.-15-67G>A | intron_variant | Intron 1 of 8 | 1 | NM_001128431.4 | ENSP00000370635.1 |
Frequencies
GnomAD3 genomes AF: 0.311 AC: 47226AN: 151692Hom.: 10160 Cov.: 31
GnomAD4 exome AF: 0.192 AC: 251871AN: 1315020Hom.: 27506 Cov.: 20 AF XY: 0.190 AC XY: 123563AN XY: 651794
GnomAD4 genome AF: 0.311 AC: 47282AN: 151812Hom.: 10176 Cov.: 31 AF XY: 0.307 AC XY: 22749AN XY: 74212
ClinVar
Submissions by phenotype
not provided Benign:2
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not specified Benign:1
This variant is classified as Benign based on local population frequency. This variant was detected in 25% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy, Progressive Myoclonus Epilepsy and Abnormal Movements and Neurodegeneration with brain iron accumulation. Number of patients: 23. Only high quality variants are reported. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at