chr5-88206508-G-GA
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_153354.5(TMEM161B):c.599-10_599-9insT variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00799 in 1,300,318 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0033 ( 2 hom., cov: 32)
Exomes 𝑓: 0.0086 ( 0 hom. )
Consequence
TMEM161B
NM_153354.5 splice_polypyrimidine_tract, intron
NM_153354.5 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.544
Genes affected
TMEM161B (HGNC:28483): (transmembrane protein 161B) Predicted to enable nucleic acid binding activity. Predicted to be involved in DNA integration. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 5-88206508-G-GA is Benign according to our data. Variant chr5-88206508-G-GA is described in ClinVar as [Benign]. Clinvar id is 2798672.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4_exome allele frequency = 0.00859 (9888/1150926) while in subpopulation AFR AF= 0.0279 (717/25656). AF 95% confidence interval is 0.0263. There are 0 homozygotes in gnomad4_exome. There are 4948 alleles in male gnomad4_exome subpopulation. Median coverage is 28. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM161B | NM_153354.5 | c.599-10_599-9insT | splice_polypyrimidine_tract_variant, intron_variant | ENST00000296595.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM161B | ENST00000296595.11 | c.599-10_599-9insT | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_153354.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00334 AC: 498AN: 149306Hom.: 2 Cov.: 32
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GnomAD4 exome AF: 0.00859 AC: 9888AN: 1150926Hom.: 0 Cov.: 28 AF XY: 0.00867 AC XY: 4948AN XY: 570702
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GnomAD4 genome AF: 0.00333 AC: 498AN: 149392Hom.: 2 Cov.: 32 AF XY: 0.00332 AC XY: 242AN XY: 72870
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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 17, 2024 | - - |
Computational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at