chr2-27256387-G-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_003459.5(SLC30A3):c.1017C>A(p.Ile339=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00107 in 1,614,012 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts 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 Benign (★).
Frequency
Consequence
NM_003459.5 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC30A3 | NM_003459.5 | c.1017C>A | p.Ile339= | splice_region_variant, synonymous_variant | 7/8 | ENST00000233535.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC30A3 | ENST00000233535.9 | c.1017C>A | p.Ile339= | splice_region_variant, synonymous_variant | 7/8 | 1 | NM_003459.5 | P1 | |
SLC30A3 | ENST00000445870.5 | c.830C>A | p.Ser277Ter | stop_gained, splice_region_variant | 6/7 | 5 | |||
SLC30A3 | ENST00000482990.1 | n.907C>A | non_coding_transcript_exon_variant | 3/3 | 2 | ||||
SLC30A3 | ENST00000497341.5 | n.1670C>A | splice_region_variant, non_coding_transcript_exon_variant | 3/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000677 AC: 103AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00204 AC: 513AN: 251218Hom.: 6 AF XY: 0.00285 AC XY: 387AN XY: 135778
GnomAD4 exome AF: 0.00111 AC: 1624AN: 1461742Hom.: 26 Cov.: 31 AF XY: 0.00158 AC XY: 1147AN XY: 727168
GnomAD4 genome AF: 0.000683 AC: 104AN: 152270Hom.: 0 Cov.: 32 AF XY: 0.00101 AC XY: 75AN XY: 74466
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 14, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at