20-45327377-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002999.4(SDC4):c.484G>A(p.Val162Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000112 in 1,613,888 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002999.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SDC4 | NM_002999.4 | c.484G>A | p.Val162Ile | missense_variant | 5/5 | ENST00000372733.3 | NP_002990.2 | |
SDC4 | XM_011528977.3 | c.268G>A | p.Val90Ile | missense_variant | 4/4 | XP_011527279.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SDC4 | ENST00000372733.3 | c.484G>A | p.Val162Ile | missense_variant | 5/5 | 1 | NM_002999.4 | ENSP00000361818.3 |
Frequencies
GnomAD3 genomes AF: 0.0000921 AC: 14AN: 152084Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000638 AC: 16AN: 250718Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135578
GnomAD4 exome AF: 0.000114 AC: 167AN: 1461688Hom.: 0 Cov.: 31 AF XY: 0.000117 AC XY: 85AN XY: 727126
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74394
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 13, 2023 | The c.484G>A (p.V162I) alteration is located in exon 5 (coding exon 5) of the SDC4 gene. This alteration results from a G to A substitution at nucleotide position 484, causing the valine (V) at amino acid position 162 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at