12-85286836-T-C
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_006982.3(ALX1):c.532-17T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00323 in 1,561,024 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0023 ( 2 hom., cov: 32)
Exomes 𝑓: 0.0033 ( 10 hom. )
Consequence
ALX1
NM_006982.3 intron
NM_006982.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0790
Genes affected
ALX1 (HGNC:1494): (ALX homeobox 1) The specific function of this gene has yet to be determined in humans; however, in rodents, it is necessary for survival of the forebrain mesenchyme and may also be involved in development of the cervix. Mutations in the mouse gene lead to neural tube defects such as acrania and meroanencephaly. [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=-0.76).
BP6
Variant 12-85286836-T-C is Benign according to our data. Variant chr12-85286836-T-C is described in ClinVar as [Benign]. Clinvar id is 1991732.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ALX1 | NM_006982.3 | c.532-17T>C | intron_variant | ENST00000316824.4 | NP_008913.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ALX1 | ENST00000316824.4 | c.532-17T>C | intron_variant | 1 | NM_006982.3 | ENSP00000315417.3 |
Frequencies
GnomAD3 genomes AF: 0.00234 AC: 355AN: 151880Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.00304 AC: 586AN: 192896Hom.: 2 AF XY: 0.00293 AC XY: 306AN XY: 104294
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GnomAD4 exome AF: 0.00332 AC: 4684AN: 1409026Hom.: 10 Cov.: 29 AF XY: 0.00317 AC XY: 2215AN XY: 698624
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GnomAD4 genome AF: 0.00234 AC: 355AN: 151998Hom.: 2 Cov.: 32 AF XY: 0.00248 AC XY: 184AN XY: 74326
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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 | Labcorp Genetics (formerly Invitae), Labcorp | Jan 19, 2024 | - - |
Computational scores
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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