chr17-41610924-C-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_005557.4(KRT16):c.989G>T(p.Arg330Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000644 in 1,614,210 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 Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R330H) has been classified as Uncertain significance.
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.989G>T | p.Arg330Leu | missense_variant | 5/8 | ENST00000301653.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRT16 | ENST00000301653.9 | c.989G>T | p.Arg330Leu | missense_variant | 5/8 | 1 | NM_005557.4 | P1 | |
KRT16 | ENST00000593067.1 | c.275G>T | p.Arg92Leu | missense_variant | 6/7 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000322 AC: 49AN: 152216Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000676 AC: 17AN: 251474Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135918
GnomAD4 exome AF: 0.0000369 AC: 54AN: 1461876Hom.: 0 Cov.: 34 AF XY: 0.0000220 AC XY: 16AN XY: 727234
GnomAD4 genome AF: 0.000328 AC: 50AN: 152334Hom.: 0 Cov.: 32 AF XY: 0.000282 AC XY: 21AN XY: 74492
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 31, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at