chr6-100447468-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005068.3(SIM1):c.851-53G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.869 in 1,608,336 control chromosomes in the GnomAD database, including 608,590 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.89 ( 60476 hom., cov: 33)
Exomes 𝑓: 0.87 ( 548114 hom. )
Consequence
SIM1
NM_005068.3 intron
NM_005068.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.958
Genes affected
SIM1 (HGNC:10882): (SIM bHLH transcription factor 1) SIM1 and SIM2 genes are Drosophila single-minded (sim) gene homologs. SIM1 transcript was detected only in fetal kidney out of various adult and fetal tissues tested. Since the sim gene plays an important role in Drosophila development and has peak levels of expression during the period of neurogenesis,it was proposed that the human SIM gene is a candidate for involvement in certain dysmorphic features (particularly the facial and skull characteristics), abnormalities of brain development, and/or cognitive disability of Down syndrome. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
Variant 6-100447468-C-T is Benign according to our data. Variant chr6-100447468-C-T is described in ClinVar as [Benign]. Clinvar id is 1246865.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.890 AC: 135367AN: 152136Hom.: 60426 Cov.: 33
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GnomAD4 exome AF: 0.867 AC: 1262165AN: 1456082Hom.: 548114 AF XY: 0.867 AC XY: 628005AN XY: 723972
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GnomAD4 genome AF: 0.890 AC: 135467AN: 152254Hom.: 60476 Cov.: 33 AF XY: 0.893 AC XY: 66467AN XY: 74442
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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
Nov 12, 2018
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Name
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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