chr15-74414831-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_003612.5(SEMA7A):c.1095+7G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000711 in 1,614,094 control chromosomes in the GnomAD database, including 8 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_003612.5 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEMA7A | NM_003612.5 | c.1095+7G>A | splice_region_variant, intron_variant | ENST00000261918.9 | |||
SEMA7A | NM_001146029.3 | c.1053+7G>A | splice_region_variant, intron_variant | ||||
SEMA7A | NM_001146030.3 | c.600+7G>A | splice_region_variant, intron_variant | ||||
SEMA7A | XM_047433177.1 | c.972+7G>A | splice_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEMA7A | ENST00000261918.9 | c.1095+7G>A | splice_region_variant, intron_variant | 1 | NM_003612.5 | P1 | |||
SEMA7A | ENST00000542748.6 | c.600+7G>A | splice_region_variant, intron_variant | 5 | |||||
SEMA7A | ENST00000543145.6 | c.1053+7G>A | splice_region_variant, intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000762 AC: 116AN: 152216Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00115 AC: 289AN: 251224Hom.: 3 AF XY: 0.00113 AC XY: 154AN XY: 135802
GnomAD4 exome AF: 0.000705 AC: 1031AN: 1461760Hom.: 8 Cov.: 32 AF XY: 0.000732 AC XY: 532AN XY: 727172
GnomAD4 genome ? AF: 0.000761 AC: 116AN: 152334Hom.: 0 Cov.: 32 AF XY: 0.000658 AC XY: 49AN XY: 74496
ClinVar
Submissions by phenotype
SEMA7A-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 12, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at