13-38686910-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_207361.6(FREM2):c.-435C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0355 in 152,238 control chromosomes in the GnomAD database, including 298 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.035 ( 298 hom., cov: 32)
Consequence
FREM2
NM_207361.6 upstream_gene
NM_207361.6 upstream_gene
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0870
Genes affected
FREM2 (HGNC:25396): (FRAS1 related extracellular matrix 2) This gene encodes an integral membrane protein containing numerous CSPG (chondroitin sulfate proteoglycan element) repeats and Calx-beta domains. The encoded protein localizes to the basement membrane, forming a ternary complex that plays a role in epidermal-dermal interactions. This protein is important for the integrity of skin and renal epithelia. Mutations in this gene are associated with Fraser syndrome. [provided by RefSeq, Apr 2014]
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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=-0.8).
BP6
Variant 13-38686910-C-T is Benign according to our data. Variant chr13-38686910-C-T is described in ClinVar as [Benign]. Clinvar id is 1243197.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FREM2 | NM_207361.6 | c.-435C>T | upstream_gene_variant | ENST00000280481.9 | NP_997244.4 | |||
FREM2 | XM_017020554.2 | c.-435C>T | upstream_gene_variant | XP_016876043.1 | ||||
LINC00437 | NR_126377.1 | n.-235G>A | upstream_gene_variant | |||||
FREM2 | XR_941571.3 | n.-167C>T | upstream_gene_variant |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0354 AC: 5388AN: 152120Hom.: 298 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0355 AC: 5404AN: 152238Hom.: 298 Cov.: 32 AF XY: 0.0342 AC XY: 2547AN XY: 74450
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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
Jun 20, 2021
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at