12-52233347-C-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
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
Genomes: 𝑓 0.0022 ( 8 hom., cov: 33)
Exomes 𝑓: 0.0015 ( 20 hom. )
Consequence
KRT7
NM_005556.4 missense
NM_005556.4 missense
Scores
2
16
Clinical Significance
Conservation
PhyloP100: 0.566
Genes affected
KRT7 (HGNC:6445): (keratin 7) The protein encoded by this gene is a member of the keratin gene family. The type II cytokeratins consist of basic or neutral proteins which are arranged in pairs of heterotypic keratin chains coexpressed during differentiation of simple and stratified epithelial tissues. This type II cytokeratin is specifically expressed in the simple epithelia lining the cavities of the internal organs and in the gland ducts and blood vessels. The genes encoding the type II cytokeratins are clustered in a region of chromosome 12q12-q13. Alternative splicing may result in several transcript variants; however, not all variants have been fully described. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0022589564).
BP6
?
Variant 12-52233347-C-A is Benign according to our data. Variant chr12-52233347-C-A is described in ClinVar as [Benign]. Clinvar id is 769820.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.00151 (2140/1419892) while in subpopulation AMR AF= 0.0228 (867/38008). AF 95% confidence interval is 0.0216. There are 20 homozygotes in gnomad4_exome. There are 943 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 8 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KRT7 | NM_005556.4 | c.51C>A | p.Phe17Leu | missense_variant | 1/9 | ENST00000331817.6 | |
KRT7 | XM_011538325.3 | c.51C>A | p.Phe17Leu | missense_variant | 1/8 | ||
KRT7 | XM_047428827.1 | c.51C>A | p.Phe17Leu | missense_variant | 1/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRT7 | ENST00000331817.6 | c.51C>A | p.Phe17Leu | missense_variant | 1/9 | 1 | NM_005556.4 | P1 | |
KRT7 | ENST00000546666.1 | n.199C>A | non_coding_transcript_exon_variant | 2/2 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00221 AC: 336AN: 152188Hom.: 8 Cov.: 33
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GnomAD3 exomes AF: 0.00639 AC: 1241AN: 194104Hom.: 12 AF XY: 0.00499 AC XY: 541AN XY: 108516
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GnomAD4 exome AF: 0.00151 AC: 2140AN: 1419892Hom.: 20 Cov.: 31 AF XY: 0.00134 AC XY: 943AN XY: 706200
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GnomAD4 genome ? AF: 0.00222 AC: 338AN: 152300Hom.: 8 Cov.: 33 AF XY: 0.00242 AC XY: 180AN XY: 74468
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Asia WGS
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 22, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
N
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MutPred
Gain of MoRF binding (P = 0.0951);
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at