chr8-117171087-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_173851.3(SLC30A8):c.883G>A(p.Asp295Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000992 in 1,612,230 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_173851.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC30A8 | NM_173851.3 | c.883G>A | p.Asp295Asn | missense_variant | 7/8 | ENST00000456015.7 | |
LOC105375716 | XR_007061067.1 | n.819+1528C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC30A8 | ENST00000456015.7 | c.883G>A | p.Asp295Asn | missense_variant | 7/8 | 1 | NM_173851.3 | P1 | |
SLC30A8 | ENST00000519688.5 | c.736G>A | p.Asp246Asn | missense_variant | 8/9 | 1 | |||
SLC30A8 | ENST00000521243.5 | c.736G>A | p.Asp246Asn | missense_variant | 9/10 | 1 | |||
SLC30A8 | ENST00000427715.2 | c.736G>A | p.Asp246Asn | missense_variant | 10/11 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000592 AC: 9AN: 152018Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000185 AC: 46AN: 249298Hom.: 0 AF XY: 0.000252 AC XY: 34AN XY: 134670
GnomAD4 exome AF: 0.000103 AC: 151AN: 1460094Hom.: 2 Cov.: 30 AF XY: 0.000142 AC XY: 103AN XY: 726360
GnomAD4 genome ? AF: 0.0000592 AC: 9AN: 152136Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 15, 2023 | The c.883G>A (p.D295N) alteration is located in exon 7 (coding exon 7) of the SLC30A8 gene. This alteration results from a G to A substitution at nucleotide position 883, causing the aspartic acid (D) at amino acid position 295 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at