rs28759013
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_020784.3(TXNDC16):c.407G>A(p.Ser136Asn) variant causes a missense change. The variant allele was found at a frequency of 0.00638 in 1,595,622 control chromosomes in the GnomAD database, including 529 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict 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_020784.3 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 |
---|---|---|---|---|---|---|---|
TXNDC16 | NM_020784.3 | c.407G>A | p.Ser136Asn | missense_variant | 7/21 | ENST00000281741.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TXNDC16 | ENST00000281741.9 | c.407G>A | p.Ser136Asn | missense_variant | 7/21 | 1 | NM_020784.3 | P1 | |
TXNDC16 | ENST00000557374.1 | c.-294-28274G>A | intron_variant | 4 | |||||
TXNDC16 | ENST00000554399.1 | n.207+33037G>A | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0345 AC: 5242AN: 151972Hom.: 268 Cov.: 32
GnomAD3 exomes AF: 0.00877 AC: 2165AN: 247004Hom.: 105 AF XY: 0.00626 AC XY: 837AN XY: 133648
GnomAD4 exome AF: 0.00341 AC: 4920AN: 1443532Hom.: 260 Cov.: 28 AF XY: 0.00294 AC XY: 2111AN XY: 718986
GnomAD4 genome ? AF: 0.0346 AC: 5261AN: 152090Hom.: 269 Cov.: 32 AF XY: 0.0331 AC XY: 2460AN XY: 74342
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at