7-155800178-C-T
Variant summary
Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_StrongBP6BS1
The ENST00000430104.5(SHH):c.369G>A(p.Pro123Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000382 in 471,242 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 (no stars).
Frequency
Consequence
ENST00000430104.5 synonymous
Scores
Clinical Significance
Conservation
Publications
- holoprosencephaly 3Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae)
- microphthalmia, isolated, with coloboma 5Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, PanelApp Australia
- polydactyly of a triphalangeal thumbInheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: G2P, Orphanet
- solitary median maxillary central incisor syndromeInheritance: AD Classification: DEFINITIVE, MODERATE Submitted by: G2P, Ambry Genetics
- skeletal system disorderInheritance: AD Classification: MODERATE Submitted by: Ambry Genetics
- autosomal dominant preaxial polydactyly-upperback hypertrichosis syndromeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- hypoplastic tibiae-postaxial polydactyly syndromeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- microphthalmia, isolated, with colobomaInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- syndactyly type 4Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- triphalangeal thumb-polysyndactyly syndromeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- holoprosencephalyInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Benign. The variant received -9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152212Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.0000800 AC: 12AN: 149936 AF XY: 0.0000372 show subpopulations
GnomAD4 exome AF: 0.0000470 AC: 15AN: 318912Hom.: 0 Cov.: 0 AF XY: 0.0000444 AC XY: 8AN XY: 180148 show subpopulations
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152330Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74486 show subpopulations
ClinVar
Submissions by phenotype
SHH-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). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at