chr12-52694772-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_175078.3(KRT77):c.934A>T(p.Thr312Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000317 in 1,607,922 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_175078.3 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 |
---|---|---|---|---|---|---|---|
KRT77 | NM_175078.3 | c.934A>T | p.Thr312Ser | missense_variant | 5/9 | ENST00000341809.8 | |
KRT77 | XM_011538288.3 | c.235A>T | p.Thr79Ser | missense_variant | 5/9 | ||
KRT77 | XM_011538289.3 | c.*91A>T | 3_prime_UTR_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRT77 | ENST00000341809.8 | c.934A>T | p.Thr312Ser | missense_variant | 5/9 | 1 | NM_175078.3 | P1 | |
KRT77 | ENST00000553168.1 | c.*272A>T | 3_prime_UTR_variant, NMD_transcript_variant | 6/10 | 1 | ||||
ENST00000547533.1 | n.351+1106T>A | intron_variant, non_coding_transcript_variant | 3 | ||||||
KRT77 | ENST00000550823.1 | n.581A>T | non_coding_transcript_exon_variant | 1/2 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 151934Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000799 AC: 2AN: 250454Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135286
GnomAD4 exome AF: 0.0000343 AC: 50AN: 1455988Hom.: 0 Cov.: 32 AF XY: 0.0000415 AC XY: 30AN XY: 723044
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 151934Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74232
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 15, 2022 | The c.934A>T (p.T312S) alteration is located in exon 5 (coding exon 5) of the KRT77 gene. This alteration results from a A to T substitution at nucleotide position 934, causing the threonine (T) at amino acid position 312 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