chr3-69104703-G-T
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1
The NM_006407.4(ARL6IP5):c.*67G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 1,560,864 control chromosomes in the GnomAD database, including 154,562 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 0.49 ( 19123 hom., cov: 30)
Exomes 𝑓: 0.43 ( 135439 hom. )
Consequence
ARL6IP5
NM_006407.4 3_prime_UTR
NM_006407.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.94
Genes affected
ARL6IP5 (HGNC:16937): (ADP ribosylation factor like GTPase 6 interacting protein 5) Expression of this gene is affected by vitamin A. The encoded protein of this gene may be associated with the cytoskeleton. A similar protein in rats may play a role in the regulation of cell differentiation. The rat protein binds and inhibits the cell membrane glutamate transporter EAAC1. The expression of the rat gene is upregulated by retinoic acid, which results in a specific reduction in EAAC1-mediated glutamate transport. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.3).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARL6IP5 | NM_006407.4 | c.*67G>T | 3_prime_UTR_variant | 3/3 | ENST00000273258.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARL6IP5 | ENST00000273258.4 | c.*67G>T | 3_prime_UTR_variant | 3/3 | 1 | NM_006407.4 | P1 | ||
ARL6IP5 | ENST00000478935.1 | c.196-135G>T | intron_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.487 AC: 73868AN: 151558Hom.: 19084 Cov.: 30
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GnomAD4 exome AF: 0.433 AC: 610416AN: 1409186Hom.: 135439 Cov.: 26 AF XY: 0.435 AC XY: 304598AN XY: 700104
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GnomAD4 genome AF: 0.488 AC: 73955AN: 151678Hom.: 19123 Cov.: 30 AF XY: 0.485 AC XY: 35927AN XY: 74088
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ClinVar
Not reported inComputational 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