chr2-43279783-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_022065.5(THADA):c.5278A>C(p.Asn1760His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000058 in 1,550,388 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022065.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
THADA | NM_022065.5 | c.5278A>C | p.Asn1760His | missense_variant | 36/38 | ENST00000405975.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
THADA | ENST00000405975.7 | c.5278A>C | p.Asn1760His | missense_variant | 36/38 | 1 | NM_022065.5 | P1 | |
THADA | ENST00000405006.8 | c.5278A>C | p.Asn1760His | missense_variant | 36/38 | 1 | P1 | ||
THADA | ENST00000407351.5 | c.2998A>C | p.Asn1000His | missense_variant | 21/23 | 2 | |||
THADA | ENST00000398653.5 | c.*4194A>C | 3_prime_UTR_variant, NMD_transcript_variant | 34/36 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152224Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000252 AC: 4AN: 158546Hom.: 0 AF XY: 0.0000120 AC XY: 1AN XY: 83392
GnomAD4 exome AF: 0.00000358 AC: 5AN: 1398164Hom.: 0 Cov.: 30 AF XY: 0.00000290 AC XY: 2AN XY: 689608
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152224Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 08, 2022 | The c.5278A>C (p.N1760H) alteration is located in exon 36 (coding exon 35) of the THADA gene. This alteration results from a A to C substitution at nucleotide position 5278, causing the asparagine (N) at amino acid position 1760 to be replaced by a histidine (H). 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