rs67357185
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_001303256.3(MORC2):c.2747+5_2747+6delAT variant causes a splice region, intron change. The variant allele was found at a frequency of 0.000571 in 1,613,960 control chromosomes in the GnomAD database, including 1 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001303256.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00306 AC: 466AN: 152126Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000776 AC: 195AN: 251242Hom.: 1 AF XY: 0.000648 AC XY: 88AN XY: 135778
GnomAD4 exome AF: 0.000308 AC: 450AN: 1461716Hom.: 0 AF XY: 0.000282 AC XY: 205AN XY: 727160
GnomAD4 genome AF: 0.00309 AC: 471AN: 152244Hom.: 1 Cov.: 33 AF XY: 0.00313 AC XY: 233AN XY: 74428
ClinVar
Submissions by phenotype
not provided Benign:3
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MORC2: BP4, BS1 -
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Charcot-Marie-Tooth disease axonal type 2Z Benign:2
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Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
MORC2-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Developmental delay, impaired growth, dysmorphic facies, and axonal neuropathy Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at