1-151135315-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_030913.6(SEMA6C):c.1434-6C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00143 in 1,612,362 control chromosomes in the GnomAD database, including 27 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_030913.6 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEMA6C | NM_030913.6 | c.1434-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000368914.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEMA6C | ENST00000368914.8 | c.1434-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_030913.6 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00771 AC: 1174AN: 152220Hom.: 17 Cov.: 33
GnomAD3 exomes AF: 0.00221 AC: 548AN: 248016Hom.: 4 AF XY: 0.00168 AC XY: 225AN XY: 134022
GnomAD4 exome AF: 0.000773 AC: 1128AN: 1460024Hom.: 10 Cov.: 32 AF XY: 0.000693 AC XY: 503AN XY: 726290
GnomAD4 genome ? AF: 0.00773 AC: 1177AN: 152338Hom.: 17 Cov.: 33 AF XY: 0.00752 AC XY: 560AN XY: 74496
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 21, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at