3-168027748-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_014498.5(GOLIM4):c.1603G>A(p.Asp535Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000212 in 1,606,040 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_014498.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GOLIM4 | ENST00000470487.6 | c.1603G>A | p.Asp535Asn | missense_variant | Exon 12 of 16 | 1 | NM_014498.5 | ENSP00000417354.1 | ||
GOLIM4 | ENST00000309027.4 | c.1519G>A | p.Asp507Asn | missense_variant | Exon 11 of 15 | 1 | ENSP00000309893.4 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151980Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251302Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135816
GnomAD4 exome AF: 0.0000220 AC: 32AN: 1454060Hom.: 0 Cov.: 29 AF XY: 0.0000304 AC XY: 22AN XY: 724224
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151980Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74224
ClinVar
Submissions by phenotype
not specified 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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at