chr4-527184-G-A
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_001127178.3(PIGG):c.2215G>A(p.Gly739Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000602 in 1,611,902 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. G739G) has been classified as Likely benign.
Frequency
Consequence
NM_001127178.3 missense
Scores
Clinical Significance
Conservation
Publications
- intellectual disability, autosomal recessive 53Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
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ACMG classification
Our verdict: Likely_benign. The variant received -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000913 AC: 139AN: 152178Hom.: 1 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.000759 AC: 188AN: 247532 AF XY: 0.000665 show subpopulations
GnomAD4 exome AF: 0.000570 AC: 832AN: 1459606Hom.: 1 Cov.: 32 AF XY: 0.000548 AC XY: 398AN XY: 725986 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.000913 AC: 139AN: 152296Hom.: 1 Cov.: 32 AF XY: 0.00134 AC XY: 100AN XY: 74460 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not provided Uncertain:1
In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -
Intellectual disability, autosomal recessive 53 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at