19-4543744-T-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_032108.4(SEMA6B):āc.2524A>Cā(p.Thr842Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000734 in 1,226,698 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_032108.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEMA6B | NM_032108.4 | c.2524A>C | p.Thr842Pro | missense_variant | 17/17 | ENST00000586582.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEMA6B | ENST00000586582.6 | c.2524A>C | p.Thr842Pro | missense_variant | 17/17 | 1 | NM_032108.4 | P1 | |
SEMA6B | ENST00000586965.1 | c.1852-648A>C | intron_variant | 1 | |||||
SEMA6B | ENST00000676793.1 | c.2524A>C | p.Thr842Pro | missense_variant | 17/17 | P1 | |||
SEMA6B | ENST00000677828.1 | c.*1786A>C | 3_prime_UTR_variant, NMD_transcript_variant | 17/17 |
Frequencies
GnomAD3 genomes ? AF: 0.0000396 AC: 6AN: 151552Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000279 AC: 3AN: 1075038Hom.: 0 Cov.: 33 AF XY: 0.00000197 AC XY: 1AN XY: 507620
GnomAD4 genome ? AF: 0.0000396 AC: 6AN: 151660Hom.: 0 Cov.: 32 AF XY: 0.0000540 AC XY: 4AN XY: 74128
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 24, 2022 | The c.2524A>C (p.T842P) alteration is located in exon 17 (coding exon 16) of the SEMA6B gene. This alteration results from a A to C substitution at nucleotide position 2524, causing the threonine (T) at amino acid position 842 to be replaced by a proline (P). 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