rs17215633
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_004212.4(SLC28A2):āc.1064T>Cā(p.Phe355Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00151 in 1,614,068 control chromosomes in the GnomAD database, including 49 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. 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 -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC28A2 | NM_004212.4 | c.1064T>C | p.Phe355Ser | missense_variant | 11/18 | ENST00000347644.8 | |
SLC28A2-AS1 | NR_120335.1 | n.27-11578A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC28A2 | ENST00000347644.8 | c.1064T>C | p.Phe355Ser | missense_variant | 11/18 | 1 | NM_004212.4 | P1 | |
SLC28A2-AS1 | ENST00000663463.1 | n.55+11621A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00831 AC: 1263AN: 152076Hom.: 27 Cov.: 31
GnomAD3 exomes AF: 0.00192 AC: 482AN: 251420Hom.: 8 AF XY: 0.00132 AC XY: 179AN XY: 135874
GnomAD4 exome AF: 0.000806 AC: 1178AN: 1461874Hom.: 22 Cov.: 32 AF XY: 0.000686 AC XY: 499AN XY: 727238
GnomAD4 genome ? AF: 0.00831 AC: 1264AN: 152194Hom.: 27 Cov.: 31 AF XY: 0.00800 AC XY: 595AN XY: 74400
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at