chr14-52457148-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020784.3(TXNDC16):c.1645A>C(p.Asn549His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000654 in 1,589,608 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020784.3 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 |
---|---|---|---|---|---|---|---|
TXNDC16 | NM_020784.3 | c.1645A>C | p.Asn549His | missense_variant | 17/21 | ENST00000281741.9 | |
TXNDC16 | NM_001160047.2 | c.1630A>C | p.Asn544His | missense_variant | 17/21 | ||
TXNDC16 | XR_007064037.1 | n.2299A>C | non_coding_transcript_exon_variant | 19/19 | |||
TXNDC16 | XR_007064038.1 | n.2175A>C | non_coding_transcript_exon_variant | 18/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TXNDC16 | ENST00000281741.9 | c.1645A>C | p.Asn549His | missense_variant | 17/21 | 1 | NM_020784.3 | P1 | |
TXNDC16 | ENST00000555312.1 | c.*163A>C | 3_prime_UTR_variant, NMD_transcript_variant | 4/5 | 5 | ||||
TXNDC16 | ENST00000554399.1 | n.208-16424A>C | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152146Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000263 AC: 6AN: 227790Hom.: 0 AF XY: 0.0000324 AC XY: 4AN XY: 123556
GnomAD4 exome AF: 0.0000682 AC: 98AN: 1437462Hom.: 0 Cov.: 28 AF XY: 0.0000630 AC XY: 45AN XY: 714818
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152146Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 01, 2022 | The c.1645A>C (p.N549H) alteration is located in exon 17 (coding exon 15) of the TXNDC16 gene. This alteration results from a A to C substitution at nucleotide position 1645, causing the asparagine (N) at amino acid position 549 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