rs17306779
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001818.5(AKR1C4):āc.105A>Gā(p.Val35=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 1,613,736 control chromosomes in the GnomAD database, including 39,315 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.19 ( 2875 hom., cov: 32)
Exomes š: 0.22 ( 36440 hom. )
Consequence
AKR1C4
NM_001818.5 synonymous
NM_001818.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.62
Genes affected
AKR1C4 (HGNC:387): (aldo-keto reductase family 1 member C4) This gene encodes a member of the aldo/keto reductase superfamily, which consists of more than 40 known enzymes and proteins. These enzymes catalyze the conversion of aldehydes and ketones to their corresponding alcohols by utilizing NADH and/or NADPH as cofactors. The enzymes display overlapping but distinct substrate specificity. This enzyme catalyzes the bioreduction of chlordecone, a toxic organochlorine pesticide, to chlordecone alcohol in liver. This gene shares high sequence identity with three other gene members and is clustered with those three genes at chromosome 10p15-p14. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BP6
?
Variant 10-5200201-A-G is Benign according to our data. Variant chr10-5200201-A-G is described in ClinVar as [Benign]. Clinvar id is 1229360.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-1.62 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AKR1C4 | NM_001818.5 | c.105A>G | p.Val35= | synonymous_variant | 2/9 | ENST00000263126.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AKR1C4 | ENST00000263126.3 | c.105A>G | p.Val35= | synonymous_variant | 2/9 | 1 | NM_001818.5 | P1 | |
AKR1C4 | ENST00000380448.5 | c.105A>G | p.Val35= | synonymous_variant | 4/11 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.187 AC: 28388AN: 152188Hom.: 2874 Cov.: 32
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GnomAD3 exomes AF: 0.205 AC: 51326AN: 250916Hom.: 5552 AF XY: 0.205 AC XY: 27749AN XY: 135606
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GnomAD4 exome AF: 0.220 AC: 320870AN: 1461430Hom.: 36440 Cov.: 32 AF XY: 0.217 AC XY: 157978AN XY: 726990
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GnomAD4 genome ? AF: 0.186 AC: 28402AN: 152306Hom.: 2875 Cov.: 32 AF XY: 0.185 AC XY: 13791AN XY: 74472
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 27, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 15, 2019 | - - |
Computational 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