1-15935976-A-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 1P and 12B. PP2BP4_StrongBS1BS2
The NM_015001.3(SPEN):āc.9736A>Gā(p.Thr3246Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000676 in 650,580 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T3246P) has been classified as Benign.
Frequency
Consequence
NM_015001.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPEN | NM_015001.3 | c.9736A>G | p.Thr3246Ala | missense_variant | 11/15 | ENST00000375759.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPEN | ENST00000375759.8 | c.9736A>G | p.Thr3246Ala | missense_variant | 11/15 | 1 | NM_015001.3 | P1 | |
SPEN | ENST00000704274.1 | c.5335A>G | p.Thr1779Ala | missense_variant | 1/4 | ||||
SPEN | ENST00000438066.2 | c.*10587A>G | 3_prime_UTR_variant, NMD_transcript_variant | 11/15 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000361 AC: 2AN: 55388Hom.: 0 Cov.: 0
GnomAD4 exome AF: 0.0000706 AC: 42AN: 595192Hom.: 0 Cov.: 31 AF XY: 0.0000535 AC XY: 16AN XY: 298870
GnomAD4 genome AF: 0.0000361 AC: 2AN: 55388Hom.: 0 Cov.: 0 AF XY: 0.0000748 AC XY: 2AN XY: 26752
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at