14-30895518-C-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001083893.2(STRN3):c.2287G>T(p.Ala763Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000316 in 1,613,964 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_001083893.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
STRN3 | ENST00000357479.10 | c.2287G>T | p.Ala763Ser | missense_variant | Exon 18 of 18 | 5 | NM_001083893.2 | ENSP00000350071.5 | ||
STRN3 | ENST00000355683.9 | c.2035G>T | p.Ala679Ser | missense_variant | Exon 16 of 16 | 1 | ENSP00000347909.5 | |||
STRN3 | ENST00000555358.5 | n.*902G>T | non_coding_transcript_exon_variant | Exon 15 of 15 | 1 | ENSP00000451028.1 | ||||
STRN3 | ENST00000555358.5 | n.*902G>T | 3_prime_UTR_variant | Exon 15 of 15 | 1 | ENSP00000451028.1 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152216Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000119 AC: 30AN: 251208Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135764
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1461748Hom.: 0 Cov.: 31 AF XY: 0.0000275 AC XY: 20AN XY: 727182
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152216Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2287G>T (p.A763S) alteration is located in exon 18 (coding exon 18) of the STRN3 gene. This alteration results from a G to T substitution at nucleotide position 2287, causing the alanine (A) at amino acid position 763 to be replaced by a serine (S). 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