chr12-52567521-A-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_175053.4(KRT74):c.1390+138T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0382 in 751,882 control chromosomes in the GnomAD database, including 734 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.032 ( 113 hom., cov: 32)
Exomes 𝑓: 0.040 ( 621 hom. )
Consequence
KRT74
NM_175053.4 intron
NM_175053.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.586
Genes affected
KRT74 (HGNC:28929): (keratin 74) Keratins are intermediate filament proteins responsible for the structural integrity of epithelial cells and are subdivided into epithelial keratins and hair keratins. This protein belongs to a family of keratins that are specifically expressed in the inner root sheath of hair follicles.[provided by RefSeq, Jun 2009]
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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 (BayesDel_noAF=-0.92).
BP6
?
Variant 12-52567521-A-T is Benign according to our data. Variant chr12-52567521-A-T is described in ClinVar as [Benign]. Clinvar id is 1273296.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0322 (4906/152242) while in subpopulation NFE AF= 0.0473 (3214/68012). AF 95% confidence interval is 0.0459. There are 113 homozygotes in gnomad4. There are 2388 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 4908 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KRT74 | NM_175053.4 | c.1390+138T>A | intron_variant | ENST00000305620.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KRT74 | ENST00000305620.3 | c.1390+138T>A | intron_variant | 1 | NM_175053.4 | P1 | |||
KRT74 | ENST00000549343.5 | c.1432+138T>A | intron_variant | 5 | |||||
KRT74 | ENST00000546384.1 | n.377+138T>A | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0323 AC: 4908AN: 152124Hom.: 113 Cov.: 32
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GnomAD4 exome AF: 0.0397 AC: 23805AN: 599640Hom.: 621 AF XY: 0.0393 AC XY: 12670AN XY: 322508
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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 | GeneDx | Jun 21, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at