chr7-134448001-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_001628.4(AKR1B1):c.720G>A(p.Lys240=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00741 in 1,613,026 control chromosomes in the GnomAD database, including 68 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0053 ( 4 hom., cov: 31)
Exomes 𝑓: 0.0076 ( 64 hom. )
Consequence
AKR1B1
NM_001628.4 synonymous
NM_001628.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0400
Genes affected
AKR1B1 (HGNC:381): (aldo-keto reductase family 1 member B) This gene encodes a member of the aldo/keto reductase superfamily, which consists of more than 40 known enzymes and proteins. This member catalyzes the reduction of a number of aldehydes, including the aldehyde form of glucose, and is thereby implicated in the development of diabetic complications by catalyzing the reduction of glucose to sorbitol. Multiple pseudogenes have been identified for this gene. The nomenclature system used by the HUGO Gene Nomenclature Committee to define human aldo-keto reductase family members is known to differ from that used by the Mouse Genome Informatics database. [provided by RefSeq, Feb 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.25).
BP6
?
Variant 7-134448001-C-T is Benign according to our data. Variant chr7-134448001-C-T is described in ClinVar as [Benign]. Clinvar id is 777632.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.04 with no splicing effect.
BS2
?
High Homozygotes in GnomAd at 4 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AKR1B1 | NM_001628.4 | c.720G>A | p.Lys240= | synonymous_variant | 7/10 | ENST00000285930.9 | |
AKR1B1 | NM_001346142.1 | c.288G>A | p.Lys96= | synonymous_variant | 7/10 | ||
AKR1B1 | NR_144376.2 | n.758G>A | non_coding_transcript_exon_variant | 7/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AKR1B1 | ENST00000285930.9 | c.720G>A | p.Lys240= | synonymous_variant | 7/10 | 1 | NM_001628.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00530 AC: 805AN: 151796Hom.: 4 Cov.: 31
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GnomAD3 exomes AF: 0.00552 AC: 1377AN: 249624Hom.: 10 AF XY: 0.00540 AC XY: 728AN XY: 134766
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GnomAD4 exome AF: 0.00763 AC: 11145AN: 1461112Hom.: 64 Cov.: 31 AF XY: 0.00725 AC XY: 5271AN XY: 726680
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GnomAD4 genome ? AF: 0.00529 AC: 804AN: 151914Hom.: 4 Cov.: 31 AF XY: 0.00511 AC XY: 379AN XY: 74204
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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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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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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