14-30911140-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001083893.2(STRN3):c.1621A>G(p.Ile541Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,613,808 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_001083893.2 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 | UniProt |
---|---|---|---|---|---|---|---|
STRN3 | NM_001083893.2 | c.1621A>G | p.Ile541Val | missense_variant | 13/18 | ENST00000357479.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STRN3 | ENST00000357479.10 | c.1621A>G | p.Ile541Val | missense_variant | 13/18 | 5 | NM_001083893.2 | P3 | |
STRN3 | ENST00000355683.9 | c.1369A>G | p.Ile457Val | missense_variant | 11/16 | 1 | A1 | ||
STRN3 | ENST00000555358.5 | c.*236A>G | 3_prime_UTR_variant, NMD_transcript_variant | 10/15 | 1 | ||||
STRN3 | ENST00000554124.2 | n.376A>G | non_coding_transcript_exon_variant | 3/5 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152172Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 251042Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135690
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461636Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 727124
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152172Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 07, 2023 | The c.1621A>G (p.I541V) alteration is located in exon 13 (coding exon 13) of the STRN3 gene. This alteration results from a A to G substitution at nucleotide position 1621, causing the isoleucine (I) at amino acid position 541 to be replaced by a valine (V). 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