chr7-80748939-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_006379.5(SEMA3C):āc.1801A>Gā(p.Ile601Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000772 in 1,613,442 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_006379.5 missense
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 |
---|---|---|---|---|---|---|---|
SEMA3C | NM_006379.5 | c.1801A>G | p.Ile601Val | missense_variant | 17/18 | ENST00000265361.8 | |
SEMA3C | NM_001350120.2 | c.1855A>G | p.Ile619Val | missense_variant | 17/18 | ||
SEMA3C | NM_001350121.2 | c.1627A>G | p.Ile543Val | missense_variant | 18/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEMA3C | ENST00000265361.8 | c.1801A>G | p.Ile601Val | missense_variant | 17/18 | 1 | NM_006379.5 | P1 | |
SEMA3C | ENST00000419255.6 | c.1801A>G | p.Ile601Val | missense_variant | 17/18 | 2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00406 AC: 617AN: 152126Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.00113 AC: 283AN: 250776Hom.: 4 AF XY: 0.000804 AC XY: 109AN XY: 135584
GnomAD4 exome AF: 0.000427 AC: 624AN: 1461198Hom.: 5 Cov.: 33 AF XY: 0.000389 AC XY: 283AN XY: 726934
GnomAD4 genome AF: 0.00408 AC: 621AN: 152244Hom.: 5 Cov.: 32 AF XY: 0.00399 AC XY: 297AN XY: 74454
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at