chr12-52608215-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_175068.3(KRT73):c.1604C>T(p.Thr535Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,458,116 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_175068.3 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 |
---|---|---|---|---|---|---|---|
KRT73 | NM_175068.3 | c.1604C>T | p.Thr535Ile | missense_variant | 9/9 | ENST00000305748.7 | |
KRT73 | XM_047428761.1 | c.1604C>T | p.Thr535Ile | missense_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRT73 | ENST00000305748.7 | c.1604C>T | p.Thr535Ile | missense_variant | 9/9 | 1 | NM_175068.3 | P1 | |
KRT73-AS1 | ENST00000551089.5 | n.102-3073G>A | intron_variant, non_coding_transcript_variant | 4 | |||||
KRT73 | ENST00000552855.1 | c.839C>T | p.Thr280Ile | missense_variant | 6/6 | 3 | |||
KRT73 | ENST00000546934.1 | n.1997C>T | non_coding_transcript_exon_variant | 8/8 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 248246Hom.: 0 AF XY: 0.00000746 AC XY: 1AN XY: 134128
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1458116Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 725280
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 29, 2023 | The c.1604C>T (p.T535I) alteration is located in exon 9 (coding exon 9) of the KRT73 gene. This alteration results from a C to T substitution at nucleotide position 1604, causing the threonine (T) at amino acid position 535 to be replaced by an isoleucine (I). 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