chr14-102922662-T-C
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The 14-102922662-T-C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 1,590,276 control chromosomes in the GnomAD database, including 180,463 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.47 ( 17105 hom., cov: 31)
Exomes 𝑓: 0.47 ( 163358 hom. )
Consequence
AMN
NM_030943.4 upstream_gene
NM_030943.4 upstream_gene
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.15
Genes affected
AMN (HGNC:14604): (amnion associated transmembrane protein) The protein encoded by this gene is a type I transmembrane protein. It is thought to modulate bone morphogenetic protein (BMP) receptor function by serving as an accessory or coreceptor, and thus facilitates or hinders BMP binding. It is known that the mouse AMN gene is expressed in the extraembryonic visceral endoderm layer during gastrulation, but it is found to be mutated in amnionless mouse. The encoded protein has sequence similarity to short gastrulation (Sog) and procollagen IIA proteins in Drosophila. [provided by RefSeq, Jul 2008]
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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=-0.84).
BP6
Variant 14-102922662-T-C is Benign according to our data. Variant chr14-102922662-T-C is described in ClinVar as [Benign]. Clinvar id is 1243841.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AMN | NM_030943.4 | upstream_gene_variant | ENST00000299155.10 | ||||
AMN | XM_011537202.4 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AMN | ENST00000299155.10 | upstream_gene_variant | 1 | NM_030943.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.471 AC: 71397AN: 151614Hom.: 17085 Cov.: 31
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GnomAD3 exomes AF: 0.440 AC: 94665AN: 215196Hom.: 21415 AF XY: 0.436 AC XY: 50933AN XY: 116826
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GnomAD4 exome AF: 0.473 AC: 680874AN: 1438544Hom.: 163358 Cov.: 40 AF XY: 0.470 AC XY: 335748AN XY: 713938
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GnomAD4 genome AF: 0.471 AC: 71462AN: 151732Hom.: 17105 Cov.: 31 AF XY: 0.469 AC XY: 34772AN XY: 74130
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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 | GeneDx | Jul 07, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at