14-21000165-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014579.4(SLC39A2):c.296A>T(p.His99Leu) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,611,136 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 17/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014579.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC39A2 | NM_014579.4 | c.296A>T | p.His99Leu | missense_variant, splice_region_variant | 3/4 | ENST00000298681.5 | |
SLC39A2 | NM_001256588.2 | c.*33A>T | splice_region_variant, 3_prime_UTR_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC39A2 | ENST00000298681.5 | c.296A>T | p.His99Leu | missense_variant, splice_region_variant | 3/4 | 1 | NM_014579.4 | P1 | |
SLC39A2 | ENST00000554422.5 | c.*33A>T | splice_region_variant, 3_prime_UTR_variant | 3/4 | 1 | ||||
ENST00000647921.1 | n.398-335T>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152164Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1458972Hom.: 0 Cov.: 29 AF XY: 0.00000138 AC XY: 1AN XY: 725962
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152164Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74348
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at