chr17-40958834-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_213656.4(KRT39):āc.1243A>Gā(p.Lys415Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000687 in 1,455,906 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_213656.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KRT39 | NM_213656.4 | c.1243A>G | p.Lys415Glu | missense_variant | 7/7 | ENST00000355612.7 | |
LOC107985072 | XR_001752886.2 | n.81-16663T>C | intron_variant, non_coding_transcript_variant | ||||
LOC107985072 | XR_001752885.2 | n.81-16663T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRT39 | ENST00000355612.7 | c.1243A>G | p.Lys415Glu | missense_variant | 7/7 | 1 | NM_213656.4 | P1 | |
KRT39 | ENST00000578078.1 | c.*732A>G | 3_prime_UTR_variant, NMD_transcript_variant | 8/8 | 1 | ||||
ENST00000418393.1 | n.386-16663T>C | intron_variant, non_coding_transcript_variant | 5 | ||||||
KRT39 | ENST00000578029.1 | n.443A>G | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000408 AC: 1AN: 245354Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 132628
GnomAD4 exome AF: 6.87e-7 AC: 1AN: 1455906Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 723690
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at