chr12-52424717-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The ENST00000252245.6(KRT75):c.1456G>A(p.Gly486Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000372 in 1,613,996 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000252245.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KRT75 | NM_004693.3 | c.1456G>A | p.Gly486Ser | missense_variant | 9/9 | ENST00000252245.6 | NP_004684.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KRT75 | ENST00000252245.6 | c.1456G>A | p.Gly486Ser | missense_variant | 9/9 | 1 | NM_004693.3 | ENSP00000252245 | P1 | |
ENST00000548135.1 | n.292-3440C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.000171 AC: 26AN: 152110Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251234Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135832
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1461768Hom.: 0 Cov.: 33 AF XY: 0.0000165 AC XY: 12AN XY: 727192
GnomAD4 genome AF: 0.000171 AC: 26AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74420
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 31, 2022 | The c.1456G>A (p.G486S) alteration is located in exon 9 (coding exon 9) of the KRT75 gene. This alteration results from a G to A substitution at nucleotide position 1456, causing the glycine (G) at amino acid position 486 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