17-40818811-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_000421.5(KRT10):c.1724G>T(p.Gly575Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00136 in 1,598,260 control chromosomes in the GnomAD database, including 8 homozygotes. 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 Benign (★).
Frequency
Consequence
NM_000421.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KRT10 | NM_000421.5 | c.1724G>T | p.Gly575Val | missense_variant | 7/8 | ENST00000269576.6 | |
KRT10 | NM_001379366.1 | c.1724G>T | p.Gly575Val | missense_variant | 7/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRT10 | ENST00000269576.6 | c.1724G>T | p.Gly575Val | missense_variant | 7/8 | 1 | NM_000421.5 | P2 | |
KRT10 | ENST00000635956.2 | c.1724G>T | p.Gly575Val | missense_variant | 7/8 | 2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00112 AC: 171AN: 152056Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00107 AC: 247AN: 230034Hom.: 0 AF XY: 0.000999 AC XY: 127AN XY: 127114
GnomAD4 exome AF: 0.00139 AC: 2006AN: 1446094Hom.: 8 Cov.: 31 AF XY: 0.00132 AC XY: 949AN XY: 719798
GnomAD4 genome ? AF: 0.00113 AC: 172AN: 152166Hom.: 0 Cov.: 33 AF XY: 0.00130 AC XY: 97AN XY: 74402
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 12, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at