rs1849929
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001286615.2(ANO4):c.1313-12050A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 313,748 control chromosomes in the GnomAD database, including 10,096 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 0.20 ( 3927 hom., cov: 32)
Exomes 𝑓: 0.26 ( 6169 hom. )
Consequence
ANO4
NM_001286615.2 intron
NM_001286615.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.722
Genes affected
ANO4 (HGNC:23837): (anoctamin 4) Enables intracellular calcium activated chloride channel activity. Involved in chloride transport. Located in plasma membrane. [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=-0.81).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANO4 | NM_001286615.2 | c.1313-12050A>T | intron_variant | ENST00000392977.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANO4 | ENST00000392977.8 | c.1313-12050A>T | intron_variant | 2 | NM_001286615.2 | ||||
SNX5P2 | ENST00000547000.1 | n.311+99A>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.200 AC: 30337AN: 151980Hom.: 3931 Cov.: 32
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GnomAD4 exome AF: 0.256 AC: 41352AN: 161650Hom.: 6169 AF XY: 0.264 AC XY: 22926AN XY: 86906
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GnomAD4 genome ? AF: 0.199 AC: 30325AN: 152098Hom.: 3927 Cov.: 32 AF XY: 0.208 AC XY: 15426AN XY: 74334
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ClinVar
Not reported inComputational scores
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Name
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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