chr12-52695781-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_175078.3(KRT77):c.906A>C(p.Leu302Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,611,754 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KRT77 | NM_175078.3 | c.906A>C | p.Leu302Phe | missense_variant | 4/9 | ENST00000341809.8 | |
KRT77 | XM_011538288.3 | c.207A>C | p.Leu69Phe | missense_variant | 4/9 | ||
KRT77 | XM_011538289.3 | c.906A>C | p.Leu302Phe | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRT77 | ENST00000341809.8 | c.906A>C | p.Leu302Phe | missense_variant | 4/9 | 1 | NM_175078.3 | P1 | |
KRT77 | ENST00000553168.1 | c.*244A>C | 3_prime_UTR_variant, NMD_transcript_variant | 5/10 | 1 | ||||
ENST00000547533.1 | n.352-598T>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152086Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251390Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135874
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1459550Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 726246
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152204Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74398
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 10, 2022 | The c.906A>C (p.L302F) alteration is located in exon 4 (coding exon 4) of the KRT77 gene. This alteration results from a A to C substitution at nucleotide position 906, causing the leucine (L) at amino acid position 302 to be replaced by a phenylalanine (F). 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