rs1042484
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_002448.3(MSX1):c.470-47A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 1,597,544 control chromosomes in the GnomAD database, including 40,406 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.20 ( 3176 hom., cov: 34)
Exomes 𝑓: 0.22 ( 37230 hom. )
Consequence
MSX1
NM_002448.3 intron
NM_002448.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.634
Genes affected
MSX1 (HGNC:7391): (msh homeobox 1) This gene encodes a member of the muscle segment homeobox gene family. The encoded protein functions as a transcriptional repressor during embryogenesis through interactions with components of the core transcription complex and other homeoproteins. It may also have roles in limb-pattern formation, craniofacial development, particularly odontogenesis, and tumor growth inhibition. Mutations in this gene, which was once known as homeobox 7, have been associated with nonsyndromic cleft lip with or without cleft palate 5, Witkop syndrome, Wolf-Hirschom syndrome, and autosomoal dominant hypodontia. [provided by RefSeq, Jul 2008]
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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=-0.83).
BP6
Variant 4-4862654-A-G is Benign according to our data. Variant chr4-4862654-A-G is described in ClinVar as [Benign]. Clinvar id is 1241303.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MSX1 | NM_002448.3 | c.470-47A>G | intron_variant | ENST00000382723.5 | NP_002439.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MSX1 | ENST00000382723.5 | c.470-47A>G | intron_variant | 1 | NM_002448.3 | ENSP00000372170 | P1 | |||
MSX1 | ENST00000468421.1 | n.181+46A>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.198 AC: 30110AN: 152052Hom.: 3177 Cov.: 34
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GnomAD3 exomes AF: 0.204 AC: 48045AN: 235490Hom.: 5239 AF XY: 0.203 AC XY: 26321AN XY: 129794
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GnomAD4 exome AF: 0.223 AC: 322526AN: 1445374Hom.: 37230 Cov.: 30 AF XY: 0.222 AC XY: 159589AN XY: 719978
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GnomAD4 genome AF: 0.198 AC: 30118AN: 152170Hom.: 3176 Cov.: 34 AF XY: 0.198 AC XY: 14710AN XY: 74408
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 13, 2021 | - - |
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