chr15-22851674-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_030922.7(NIPA2):c.-58C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0241 in 1,455,732 control chromosomes in the GnomAD database, including 590 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.019 ( 45 hom., cov: 32)
Exomes 𝑓: 0.025 ( 545 hom. )
Consequence
NIPA2
NM_030922.7 5_prime_UTR
NM_030922.7 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.568
Genes affected
NIPA2 (HGNC:17044): (NIPA magnesium transporter 2) This gene encodes a possible magnesium transporter. This gene is located adjacent to the imprinted domain in the Prader-Willi syndrome deletion region of chromosome 15. Alternate splicing results in multiple transcript variants. Pseudogenes of this gene are found on chromosomes 3, 7 and 21.[provided by RefSeq, May 2010]
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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=-0.83).
BP6
?
Variant 15-22851674-C-T is Benign according to our data. Variant chr15-22851674-C-T is described in ClinVar as [Benign]. Clinvar id is 1248113.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0193 (2935/152188) while in subpopulation NFE AF= 0.0247 (1680/68000). AF 95% confidence interval is 0.0237. There are 45 homozygotes in gnomad4. There are 1518 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 45 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NIPA2 | NM_030922.7 | c.-58C>T | 5_prime_UTR_variant | 4/8 | ENST00000337451.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NIPA2 | ENST00000337451.8 | c.-58C>T | 5_prime_UTR_variant | 4/8 | 5 | NM_030922.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0193 AC: 2935AN: 152070Hom.: 45 Cov.: 32
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GnomAD4 exome AF: 0.0247 AC: 32134AN: 1303544Hom.: 545 Cov.: 17 AF XY: 0.0243 AC XY: 15803AN XY: 650708
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GnomAD4 genome ? AF: 0.0193 AC: 2935AN: 152188Hom.: 45 Cov.: 32 AF XY: 0.0204 AC XY: 1518AN XY: 74384
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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 | May 13, 2021 | - - |
Computational scores
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Name
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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