17-40962209-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_213656.4(KRT39):c.949C>T(p.Arg317Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000217 in 1,614,064 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R317L) has been classified as Uncertain significance.
Frequency
Consequence
NM_213656.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KRT39 | NM_213656.4 | c.949C>T | p.Arg317Cys | missense_variant | 5/7 | ENST00000355612.7 | |
LOC107985072 | XR_001752886.2 | n.81-13288G>A | intron_variant, non_coding_transcript_variant | ||||
LOC107985072 | XR_001752885.2 | n.81-13288G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRT39 | ENST00000355612.7 | c.949C>T | p.Arg317Cys | missense_variant | 5/7 | 1 | NM_213656.4 | P1 | |
KRT39 | ENST00000578078.1 | c.*438C>T | 3_prime_UTR_variant, NMD_transcript_variant | 6/8 | 1 | ||||
ENST00000418393.1 | n.386-13288G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152202Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251282Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135786
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461862Hom.: 0 Cov.: 32 AF XY: 0.0000193 AC XY: 14AN XY: 727232
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152202Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 13, 2023 | The c.949C>T (p.R317C) alteration is located in exon 5 (coding exon 5) of the KRT39 gene. This alteration results from a C to T substitution at nucleotide position 949, causing the arginine (R) at amino acid position 317 to be replaced by a cysteine (C). 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