chr17-41620713-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The NM_000422.3(KRT17):c.1127G>A(p.Arg376Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000881 in 1,612,252 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R376W) has been classified as Likely benign.
Frequency
Consequence
NM_000422.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KRT17 | NM_000422.3 | c.1127G>A | p.Arg376Gln | missense_variant | 6/8 | ENST00000311208.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRT17 | ENST00000311208.13 | c.1127G>A | p.Arg376Gln | missense_variant | 6/8 | 1 | NM_000422.3 | P1 | |
KRT17 | ENST00000648859.1 | c.119G>A | p.Arg40Gln | missense_variant | 1/2 | ||||
KRT17 | ENST00000493253.5 | n.1514G>A | non_coding_transcript_exon_variant | 5/7 | 2 | ||||
KRT17 | ENST00000649249.1 | n.403G>A | non_coding_transcript_exon_variant | 2/4 |
Frequencies
GnomAD3 genomes AF: 0.000328 AC: 50AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000112 AC: 28AN: 250734Hom.: 0 AF XY: 0.0000811 AC XY: 11AN XY: 135676
GnomAD4 exome AF: 0.0000630 AC: 92AN: 1459914Hom.: 0 Cov.: 36 AF XY: 0.0000413 AC XY: 30AN XY: 726266
GnomAD4 genome AF: 0.000328 AC: 50AN: 152338Hom.: 0 Cov.: 32 AF XY: 0.000349 AC XY: 26AN XY: 74494
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at