15-74410681-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1
The NM_003612.5(SEMA7A):c.1944C>T(p.Ala648Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0704 in 1,609,660 control chromosomes in the GnomAD database, including 7,574 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_003612.5 synonymous
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SEMA7A | NM_003612.5 | c.1944C>T | p.Ala648Ala | synonymous_variant | Exon 14 of 14 | ENST00000261918.9 | NP_003603.1 | |
SEMA7A | NM_001146029.3 | c.1902C>T | p.Ala634Ala | synonymous_variant | Exon 13 of 13 | NP_001139501.1 | ||
SEMA7A | NM_001146030.3 | c.1449C>T | p.Ala483Ala | synonymous_variant | Exon 14 of 14 | NP_001139502.1 | ||
SEMA7A | XM_047433177.1 | c.1821C>T | p.Ala607Ala | synonymous_variant | Exon 14 of 14 | XP_047289133.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SEMA7A | ENST00000261918.9 | c.1944C>T | p.Ala648Ala | synonymous_variant | Exon 14 of 14 | 1 | NM_003612.5 | ENSP00000261918.4 | ||
SEMA7A | ENST00000543145.6 | c.1902C>T | p.Ala634Ala | synonymous_variant | Exon 13 of 13 | 2 | ENSP00000438966.2 | |||
SEMA7A | ENST00000542748.6 | c.1449C>T | p.Ala483Ala | synonymous_variant | Exon 14 of 14 | 5 | ENSP00000441493.1 |
Frequencies
GnomAD3 genomes AF: 0.135 AC: 20537AN: 152164Hom.: 2530 Cov.: 32
GnomAD3 exomes AF: 0.0846 AC: 21106AN: 249526Hom.: 1775 AF XY: 0.0826 AC XY: 11155AN XY: 134970
GnomAD4 exome AF: 0.0637 AC: 92778AN: 1457378Hom.: 5041 Cov.: 32 AF XY: 0.0643 AC XY: 46556AN XY: 724140
GnomAD4 genome AF: 0.135 AC: 20564AN: 152282Hom.: 2533 Cov.: 32 AF XY: 0.135 AC XY: 10051AN XY: 74466
ClinVar
Submissions by phenotype
SEMA7A-related disorder Benign:1
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