chr17-58208136-T-C
Variant summary
Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_ModerateBP6_Very_StrongBP7
The NM_017777.4(MKS1):c.1134A>G(p.Glu378Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000107 in 1,613,968 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_017777.4 synonymous
Scores
Clinical Significance
Conservation
Publications
- Meckel syndrome, type 1Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Myriad Women’s Health, Labcorp Genetics (formerly Invitae)
- Bardet-Biedl syndrome 13Inheritance: Unknown, AR Classification: DEFINITIVE, STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp, G2P
- Joubert syndrome 28Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
- Bardet-Biedl syndromeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- Joubert syndromeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- Joubert syndrome with ocular defectInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- Meckel syndromeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Benign. The variant received -11 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152146Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000160 AC: 4AN: 249560 AF XY: 0.0000222 show subpopulations
GnomAD4 exome AF: 0.000110 AC: 161AN: 1461704Hom.: 0 Cov.: 32 AF XY: 0.000117 AC XY: 85AN XY: 727164 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0000722 AC: 11AN: 152264Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74450 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
Meckel syndrome, type 1 Uncertain:1
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not specified Benign:1
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not provided Benign:1
MKS1: BP4, BP7 -
MKS1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Meckel-Gruber syndrome;C0431399:Joubert syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at