7-27799984-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006024.7(TAX1BP1):c.1658A>G(p.Asn553Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000207 in 1,446,076 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_006024.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAX1BP1 | NM_006024.7 | c.1658A>G | p.Asn553Ser | missense_variant | 13/17 | ENST00000396319.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAX1BP1 | ENST00000396319.7 | c.1658A>G | p.Asn553Ser | missense_variant | 13/17 | 1 | NM_006024.7 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000420 AC: 1AN: 237834Hom.: 0 AF XY: 0.00000778 AC XY: 1AN XY: 128546
GnomAD4 exome AF: 0.00000207 AC: 3AN: 1446076Hom.: 0 Cov.: 30 AF XY: 0.00000139 AC XY: 1AN XY: 718958
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 21, 2023 | The c.1658A>G (p.N553S) alteration is located in exon 13 (coding exon 12) of the TAX1BP1 gene. This alteration results from a A to G substitution at nucleotide position 1658, causing the asparagine (N) at amino acid position 553 to be replaced by a serine (S). 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