rs61997174
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_207361.6(FREM2):c.1188G>A(p.Gln396=) variant causes a synonymous change. The variant allele was found at a frequency of 0.000000684 in 1,461,696 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
FREM2
NM_207361.6 synonymous
NM_207361.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.89
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 Likely_benign. Variant got -4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BP6
?
Variant 13-38688532-G-A is Benign according to our data. Variant chr13-38688532-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2793478.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FREM2 | NM_207361.6 | c.1188G>A | p.Gln396= | synonymous_variant | 1/24 | ENST00000280481.9 | |
FREM2 | XM_017020554.2 | c.1188G>A | p.Gln396= | synonymous_variant | 1/3 | ||
FREM2 | XR_941571.3 | n.1456G>A | non_coding_transcript_exon_variant | 1/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FREM2 | ENST00000280481.9 | c.1188G>A | p.Gln396= | synonymous_variant | 1/24 | 1 | NM_207361.6 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
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32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251060Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135722
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GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461696Hom.: 0 Cov.: 46 AF XY: 0.00 AC XY: 0AN XY: 727136
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GnomAD4 genome ? Cov.: 32
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 30, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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