chr12-52233347-C-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_005556.4(KRT7):c.51C>A(p.Phe17Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00158 in 1,572,192 control chromosomes in the GnomAD database, including 28 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_005556.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KRT7 | NM_005556.4 | c.51C>A | p.Phe17Leu | missense_variant | Exon 1 of 9 | ENST00000331817.6 | NP_005547.3 | |
KRT7 | XM_011538325.3 | c.51C>A | p.Phe17Leu | missense_variant | Exon 1 of 8 | XP_011536627.1 | ||
KRT7 | XM_047428827.1 | c.51C>A | p.Phe17Leu | missense_variant | Exon 1 of 7 | XP_047284783.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00221 AC: 336AN: 152188Hom.: 8 Cov.: 33
GnomAD3 exomes AF: 0.00639 AC: 1241AN: 194104Hom.: 12 AF XY: 0.00499 AC XY: 541AN XY: 108516
GnomAD4 exome AF: 0.00151 AC: 2140AN: 1419892Hom.: 20 Cov.: 31 AF XY: 0.00134 AC XY: 943AN XY: 706200
GnomAD4 genome AF: 0.00222 AC: 338AN: 152300Hom.: 8 Cov.: 33 AF XY: 0.00242 AC XY: 180AN XY: 74468
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jun 22, 2018 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at