chr3-43079574-G-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_032806.6(POMGNT2):c.*115C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00379 in 896,214 control chromosomes in the GnomAD database, including 76 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.015 ( 56 hom., cov: 33)
Exomes 𝑓: 0.0016 ( 20 hom. )
Consequence
POMGNT2
NM_032806.6 3_prime_UTR
NM_032806.6 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.751
Genes affected
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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=-0.86).
BP6
?
Variant 3-43079574-G-T is Benign according to our data. Variant chr3-43079574-G-T is described in ClinVar as [Benign]. Clinvar id is 1222363.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0145 (2215/152334) while in subpopulation AFR AF= 0.0505 (2101/41564). AF 95% confidence interval is 0.0487. There are 56 homozygotes in gnomad4. There are 1028 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 54 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POMGNT2 | NM_032806.6 | c.*115C>A | 3_prime_UTR_variant | 2/2 | ENST00000344697.3 | ||
POMGNT2 | XM_005265515.4 | c.*115C>A | 3_prime_UTR_variant | 3/3 | |||
POMGNT2 | XM_011534163.3 | c.*115C>A | 3_prime_UTR_variant | 3/3 | |||
POMGNT2 | XM_017007353.2 | c.*115C>A | 3_prime_UTR_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POMGNT2 | ENST00000344697.3 | c.*115C>A | 3_prime_UTR_variant | 2/2 | 1 | NM_032806.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0145 AC: 2208AN: 152216Hom.: 54 Cov.: 33
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GnomAD4 exome AF: 0.00159 AC: 1185AN: 743880Hom.: 20 Cov.: 10 AF XY: 0.00131 AC XY: 496AN XY: 379052
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GnomAD4 genome ? AF: 0.0145 AC: 2215AN: 152334Hom.: 56 Cov.: 33 AF XY: 0.0138 AC XY: 1028AN XY: 74496
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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 | Apr 03, 2019 | - - |
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