17-41610000-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_005557.4(KRT16):c.1357C>T(p.Arg453Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000571 in 1,611,718 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_005557.4 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 | UniProt |
---|---|---|---|---|---|---|---|
KRT16 | NM_005557.4 | c.1357C>T | p.Arg453Cys | missense_variant | 8/8 | ENST00000301653.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRT16 | ENST00000301653.9 | c.1357C>T | p.Arg453Cys | missense_variant | 8/8 | 1 | NM_005557.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000959 AC: 24AN: 250154Hom.: 1 AF XY: 0.000148 AC XY: 20AN XY: 135352
GnomAD4 exome AF: 0.0000582 AC: 85AN: 1459534Hom.: 1 Cov.: 31 AF XY: 0.0000785 AC XY: 57AN XY: 726094
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74354
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at