chr20-6075048-TG-T
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BS1_SupportingBS2
The NM_017671.5(FERMT1):c.*2124del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0123 in 137,926 control chromosomes in the GnomAD database, including 43 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.012 ( 43 hom., cov: 23)
Exomes 𝑓: 0.0082 ( 0 hom. )
Consequence
FERMT1
NM_017671.5 3_prime_UTR
NM_017671.5 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -1.13
Genes affected
FERMT1 (HGNC:15889): (FERM domain containing kindlin 1) This gene encodes a member of the fermitin family, and contains a FERM domain and a pleckstrin homology domain. The encoded protein is involved in integrin signaling and linkage of the actin cytoskeleton to the extracellular matrix. Mutations in this gene have been linked to Kindler syndrome. [provided by RefSeq, Dec 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0123 (1701/137804) while in subpopulation AFR AF= 0.0426 (1478/34660). AF 95% confidence interval is 0.0408. There are 43 homozygotes in gnomad4. There are 756 alleles in male gnomad4 subpopulation. Median coverage is 23. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
BS2
High Homozygotes in GnomAd4 at 43 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FERMT1 | NM_017671.5 | c.*2124del | 3_prime_UTR_variant | 15/15 | ENST00000217289.9 | NP_060141.3 | ||
FERMT1 | XM_024451935.2 | c.*2124del | 3_prime_UTR_variant | 15/15 | XP_024307703.1 | |||
FERMT1 | XM_047440259.1 | c.*2124del | 3_prime_UTR_variant | 15/15 | XP_047296215.1 | |||
FERMT1 | XM_047440260.1 | c.*2124del | 3_prime_UTR_variant | 14/14 | XP_047296216.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FERMT1 | ENST00000217289.9 | c.*2124del | 3_prime_UTR_variant | 15/15 | 1 | NM_017671.5 | ENSP00000217289 | P1 | ||
FERMT1 | ENST00000478194.1 | n.3118del | non_coding_transcript_exon_variant | 7/7 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0124 AC: 1702AN: 137726Hom.: 43 Cov.: 23
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GnomAD4 exome AF: 0.00820 AC: 1AN: 122Hom.: 0 Cov.: 0 AF XY: 0.0139 AC XY: 1AN XY: 72
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GnomAD4 genome AF: 0.0123 AC: 1701AN: 137804Hom.: 43 Cov.: 23 AF XY: 0.0113 AC XY: 756AN XY: 67060
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Kindler syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at