17-41516215-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_002275.4(KRT15):c.789G>A(p.Met263Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,614,038 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002275.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KRT15 | NM_002275.4 | c.789G>A | p.Met263Ile | missense_variant | Exon 4 of 8 | ENST00000254043.8 | NP_002266.3 | |
KRT15 | XM_011524784.4 | c.810G>A | p.Met270Ile | missense_variant | Exon 4 of 8 | XP_011523086.1 | ||
KRT15 | XM_017024614.3 | c.810G>A | p.Met270Ile | missense_variant | Exon 4 of 8 | XP_016880103.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251222Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135744
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461838Hom.: 1 Cov.: 32 AF XY: 0.0000234 AC XY: 17AN XY: 727222
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.789G>A (p.M263I) alteration is located in exon 4 (coding exon 4) of the KRT15 gene. This alteration results from a G to A substitution at nucleotide position 789, causing the methionine (M) at amino acid position 263 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at