7-83977202-G-A
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1
The NM_006080.3(SEMA3A):c.1653-6C>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 0.788 in 1,552,192 control chromosomes in the GnomAD database, including 485,009 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_006080.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEMA3A | NM_006080.3 | c.1653-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000265362.9 | |||
SEMA3A | XM_005250110.4 | c.1653-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
SEMA3A | XM_047419751.1 | c.1653-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEMA3A | ENST00000265362.9 | c.1653-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_006080.3 | P1 | |||
SEMA3A | ENST00000436949.5 | c.1653-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.825 AC: 125272AN: 151856Hom.: 52367 Cov.: 31
GnomAD3 exomes AF: 0.788 AC: 186776AN: 236956Hom.: 74353 AF XY: 0.780 AC XY: 100379AN XY: 128716
GnomAD4 exome AF: 0.784 AC: 1098096AN: 1400220Hom.: 432570 Cov.: 23 AF XY: 0.783 AC XY: 546392AN XY: 697954
GnomAD4 genome AF: 0.825 AC: 125406AN: 151972Hom.: 52439 Cov.: 31 AF XY: 0.817 AC XY: 60700AN XY: 74278
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 09, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at