chr12-52618518-G-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_175068.3(KRT73):c.7C>T(p.Arg3Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000956 in 1,597,616 control chromosomes in the GnomAD database, including 55 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00055 ( 6 hom., cov: 33)
Exomes 𝑓: 0.0010 ( 49 hom. )
Consequence
KRT73
NM_175068.3 missense
NM_175068.3 missense
Scores
2
6
10
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.169
Genes affected
KRT73 (HGNC:28928): (keratin 73) Keratins are intermediate filament proteins responsible for the structural integrity of epithelial cells and are subdivided into epithelial keratins and hair keratins. This gene encodes a protein that is expressed in the inner root sheath of hair follicles. The type II keratins are clustered in a region of chromosome 12q13.[provided by RefSeq, Jun 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.016466051).
BS1
?
Variant frequency is greater than expected in population eas. gnomad4_exome allele frequency = 0.001 (1445/1445330) while in subpopulation EAS AF= 0.034 (1342/39456). AF 95% confidence interval is 0.0325. There are 49 homozygotes in gnomad4_exome. There are 701 alleles in male gnomad4_exome subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 6 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KRT73 | NM_175068.3 | c.7C>T | p.Arg3Cys | missense_variant | 1/9 | ENST00000305748.7 | |
KRT73 | XM_047428761.1 | c.7C>T | p.Arg3Cys | missense_variant | 3/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRT73 | ENST00000305748.7 | c.7C>T | p.Arg3Cys | missense_variant | 1/9 | 1 | NM_175068.3 | P1 | |
KRT73 | ENST00000546934.1 | n.32C>T | non_coding_transcript_exon_variant | 1/8 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000545 AC: 83AN: 152168Hom.: 6 Cov.: 33
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GnomAD3 exomes AF: 0.000232 AC: 55AN: 237038Hom.: 0 AF XY: 0.000203 AC XY: 26AN XY: 128370
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GnomAD4 exome AF: 0.00100 AC: 1445AN: 1445330Hom.: 49 Cov.: 32 AF XY: 0.000978 AC XY: 701AN XY: 717128
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GnomAD4 genome ? AF: 0.000545 AC: 83AN: 152286Hom.: 6 Cov.: 33 AF XY: 0.000631 AC XY: 47AN XY: 74466
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Asia WGS
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Pathogenic
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
D
MetaRNN
Benign
T
MetaSVM
Uncertain
D
MutationAssessor
Benign
L
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D
REVEL
Uncertain
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
MVP
MPC
ClinPred
T
GERP RS
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at