chr6-84089072-A-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_138409.4(MRAP2):c.228-19A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00177 in 1,588,048 control chromosomes in the GnomAD database, including 27 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0068 ( 14 hom., cov: 32)
Exomes 𝑓: 0.0012 ( 13 hom. )
Consequence
MRAP2
NM_138409.4 intron
NM_138409.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.48
Genes affected
MRAP2 (HGNC:21232): (melanocortin 2 receptor accessory protein 2) This gene encodes a protein that modulates melanocortin receptor signaling. The encoded protein has been shown to interact with all known melanocortin receptors and may regulate both receptor trafficking and activation in response to ligands. Mice lacking a functional copy of this gene exhibit severe obesity and a mutation in this gene may be associated with severe obesity in human patients. [provided by RefSeq, Oct 2016]
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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=-1.04).
BP6
?
Variant 6-84089072-A-C is Benign according to our data. Variant chr6-84089072-A-C is described in ClinVar as [Benign]. Clinvar id is 1601123.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0068 (1035/152168) while in subpopulation AFR AF= 0.0221 (919/41528). AF 95% confidence interval is 0.0209. There are 14 homozygotes in gnomad4. There are 504 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1036 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MRAP2 | NM_138409.4 | c.228-19A>C | intron_variant | ENST00000257776.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MRAP2 | ENST00000257776.5 | c.228-19A>C | intron_variant | 1 | NM_138409.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00681 AC: 1036AN: 152050Hom.: 14 Cov.: 32
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GnomAD3 exomes AF: 0.00222 AC: 507AN: 228200Hom.: 7 AF XY: 0.00178 AC XY: 221AN XY: 124022
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GnomAD4 exome AF: 0.00124 AC: 1777AN: 1435880Hom.: 13 Cov.: 30 AF XY: 0.00116 AC XY: 827AN XY: 712752
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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 | Invitae | Jan 03, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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