17-41619622-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_000422.3(KRT17):c.1271G>A(p.Arg424His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000171 in 1,612,166 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000422.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KRT17 | NM_000422.3 | c.1271G>A | p.Arg424His | missense_variant | 8/8 | ENST00000311208.13 | NP_000413.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KRT17 | ENST00000311208.13 | c.1271G>A | p.Arg424His | missense_variant | 8/8 | 1 | NM_000422.3 | ENSP00000308452 | P1 | |
KRT17 | ENST00000493253.5 | n.1658G>A | non_coding_transcript_exon_variant | 7/7 | 2 | |||||
KRT17 | ENST00000649249.1 | n.547G>A | non_coding_transcript_exon_variant | 4/4 |
Frequencies
GnomAD3 genomes AF: 0.000171 AC: 26AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000175 AC: 44AN: 251090Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 135726
GnomAD4 exome AF: 0.000171 AC: 250AN: 1459894Hom.: 0 Cov.: 32 AF XY: 0.000160 AC XY: 116AN XY: 726246
GnomAD4 genome AF: 0.000171 AC: 26AN: 152272Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74460
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 19, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at