rs1060896
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_004212.4(SLC28A2):c.225C>A(p.Ser75Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.598 in 1,610,694 control chromosomes in the GnomAD database, including 308,023 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_004212.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC28A2 | NM_004212.4 | c.225C>A | p.Ser75Arg | missense_variant | 4/18 | ENST00000347644.8 | |
SLC28A2-AS1 | NR_120335.1 | n.27-6071G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC28A2 | ENST00000347644.8 | c.225C>A | p.Ser75Arg | missense_variant | 4/18 | 1 | NM_004212.4 | P1 | |
SLC28A2-AS1 | ENST00000663463.1 | n.55+17128G>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.473 AC: 71905AN: 151958Hom.: 20722 Cov.: 31
GnomAD3 exomes AF: 0.501 AC: 125660AN: 251060Hom.: 36498 AF XY: 0.518 AC XY: 70311AN XY: 135670
GnomAD4 exome AF: 0.611 AC: 890706AN: 1458618Hom.: 287307 Cov.: 34 AF XY: 0.610 AC XY: 442642AN XY: 725744
GnomAD4 genome ? AF: 0.473 AC: 71898AN: 152076Hom.: 20716 Cov.: 31 AF XY: 0.464 AC XY: 34527AN XY: 74344
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 18, 2019 | This variant is associated with the following publications: (PMID: 30315176) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at