7-21429536-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001326543.2(SP4):c.-569C>T variant causes a 5 prime UTR premature start codon gain change. The variant allele was found at a frequency of 0.00000248 in 1,613,778 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 Uncertain significance (★).
Frequency
Consequence
NM_001326543.2 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SP4 | ENST00000222584.8 | c.371C>T | p.Ser124Leu | missense_variant | Exon 3 of 6 | 1 | NM_003112.5 | ENSP00000222584.3 | ||
SP4 | ENST00000649633.1 | c.320C>T | p.Ser107Leu | missense_variant | Exon 3 of 6 | ENSP00000496957.1 | ||||
SP4 | ENST00000432066.2 | c.7+1278C>T | intron_variant | Intron 1 of 1 | 5 | ENSP00000393623.2 | ||||
SP4 | ENST00000448246.1 | n.123+744C>T | intron_variant | Intron 2 of 4 | 5 | ENSP00000390817.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251468Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135916
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461594Hom.: 0 Cov.: 35 AF XY: 0.00000138 AC XY: 1AN XY: 727110
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.371C>T (p.S124L) alteration is located in exon 3 (coding exon 3) of the SP4 gene. This alteration results from a C to T substitution at nucleotide position 371, causing the serine (S) at amino acid position 124 to be replaced by a leucine (L). 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