20-6075709-G-A
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_017671.5(FERMT1):c.*1464C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,224 control chromosomes in the GnomAD database, including 4,886 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.24 ( 4881 hom., cov: 32)
Exomes 𝑓: 0.18 ( 5 hom. )
Consequence
FERMT1
NM_017671.5 3_prime_UTR
NM_017671.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.36
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 Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
Variant 20-6075709-G-A is Benign according to our data. Variant chr20-6075709-G-A is described in ClinVar as [Benign]. Clinvar id is 339180.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FERMT1 | NM_017671.5 | c.*1464C>T | 3_prime_UTR_variant | 15/15 | ENST00000217289.9 | NP_060141.3 | ||
FERMT1 | XM_024451935.2 | c.*1464C>T | 3_prime_UTR_variant | 15/15 | XP_024307703.1 | |||
FERMT1 | XM_047440259.1 | c.*1464C>T | 3_prime_UTR_variant | 15/15 | XP_047296215.1 | |||
FERMT1 | XM_047440260.1 | c.*1464C>T | 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.*1464C>T | 3_prime_UTR_variant | 15/15 | 1 | NM_017671.5 | ENSP00000217289 | P1 | ||
FERMT1 | ENST00000478194.1 | n.2458C>T | non_coding_transcript_exon_variant | 7/7 | 1 | |||||
FERMT1 | ENST00000699095.1 | c.*1464C>T | 3_prime_UTR_variant | 14/14 | ENSP00000514127 | P1 |
Frequencies
GnomAD3 genomes AF: 0.240 AC: 36483AN: 151942Hom.: 4855 Cov.: 32
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GnomAD4 exome AF: 0.183 AC: 30AN: 164Hom.: 5 Cov.: 0 AF XY: 0.177 AC XY: 17AN XY: 96
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GnomAD4 genome AF: 0.240 AC: 36565AN: 152060Hom.: 4881 Cov.: 32 AF XY: 0.242 AC XY: 18017AN XY: 74326
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Kindler syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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