chr5-75611679-GGGGCTGCTGCTCC-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_001276713.2(ANKDD1B):c.56_68del(p.Leu19ArgfsTer75) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0018 in 1,231,796 control chromosomes in the GnomAD database, including 34 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0086 ( 22 hom., cov: 31)
Exomes 𝑓: 0.00084 ( 12 hom. )
Consequence
ANKDD1B
NM_001276713.2 frameshift
NM_001276713.2 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.11
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 5-75611679-GGGGCTGCTGCTCC-G is Benign according to our data. Variant chr5-75611679-GGGGCTGCTGCTCC-G is described in ClinVar as [Benign]. Clinvar id is 768006.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00859 (1308/152252) while in subpopulation AFR AF= 0.0301 (1252/41564). AF 95% confidence interval is 0.0287. There are 22 homozygotes in gnomad4. There are 624 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 22 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANKDD1B | NM_001276713.2 | c.56_68del | p.Leu19ArgfsTer75 | frameshift_variant | 1/14 | ENST00000601380.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKDD1B | ENST00000601380.4 | c.56_68del | p.Leu19ArgfsTer75 | frameshift_variant | 1/14 | 5 | NM_001276713.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00855 AC: 1300AN: 152134Hom.: 22 Cov.: 31
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GnomAD3 exomes AF: 0.00376 AC: 1AN: 266Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 158
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GnomAD4 exome AF: 0.000840 AC: 907AN: 1079544Hom.: 12 AF XY: 0.000738 AC XY: 376AN XY: 509732
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GnomAD4 genome ? AF: 0.00859 AC: 1308AN: 152252Hom.: 22 Cov.: 31 AF XY: 0.00838 AC XY: 624AN XY: 74446
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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 | Dec 31, 2019 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at