chr3-126611042-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_052883.3(TXNRD3):c.1723G>T(p.Asp575Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.000185 in 1,504,740 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D575V) has been classified as Uncertain significance.
Frequency
Consequence
NM_052883.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TXNRD3 | NM_052883.3 | c.1723G>T | p.Asp575Tyr | missense_variant | 14/16 | ENST00000524230.9 | |
TXNRD3 | NM_001173513.3 | c.1615G>T | p.Asp539Tyr | missense_variant | 13/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TXNRD3 | ENST00000524230.9 | c.1723G>T | p.Asp575Tyr | missense_variant | 14/16 | 1 | NM_052883.3 | P1 | |
TXNRD3 | ENST00000523403.3 | c.1615G>T | p.Asp539Tyr | missense_variant | 13/15 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000375 AC: 57AN: 152126Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000316 AC: 39AN: 123322Hom.: 0 AF XY: 0.000372 AC XY: 25AN XY: 67162
GnomAD4 exome AF: 0.000164 AC: 222AN: 1352496Hom.: 2 Cov.: 26 AF XY: 0.000168 AC XY: 112AN XY: 666916
GnomAD4 genome AF: 0.000374 AC: 57AN: 152244Hom.: 1 Cov.: 32 AF XY: 0.000618 AC XY: 46AN XY: 74438
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 17, 2022 | The c.1723G>T (p.D575Y) alteration is located in exon 14 (coding exon 14) of the TXNRD3 gene. This alteration results from a G to T substitution at nucleotide position 1723, causing the aspartic acid (D) at amino acid position 575 to be replaced by a tyrosine (Y). 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