rs4805784
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_032139.3(ANKRD27):c.1420+223G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.668 in 152,182 control chromosomes in the GnomAD database, including 34,167 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.67 ( 34167 hom., cov: 35)
Consequence
ANKRD27
NM_032139.3 intron
NM_032139.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -4.21
Genes affected
ANKRD27 (HGNC:25310): (ankyrin repeat domain 27) Enables guanyl-nucleotide exchange factor activity and small GTPase binding activity. Involved in endocytic recycling and negative regulation of SNARE complex assembly. Acts upstream of or within early endosome to late endosome transport. Located in endosome; lysosome; and plasma membrane. Implicated in eosinophilic esophagitis. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANKRD27 | NM_032139.3 | c.1420+223G>T | intron_variant | ENST00000306065.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKRD27 | ENST00000306065.9 | c.1420+223G>T | intron_variant | 1 | NM_032139.3 | P1 | |||
ANKRD27 | ENST00000591100.6 | c.502+223G>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.668 AC: 101624AN: 152064Hom.: 34137 Cov.: 35
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.668 AC: 101696AN: 152182Hom.: 34167 Cov.: 35 AF XY: 0.663 AC XY: 49357AN XY: 74392
GnomAD4 genome
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49357
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74392
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2067
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at