chr7-84999837-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001384900.1(SEMA3D):c.1937C>T(p.Thr646Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000247 in 1,613,122 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. T646T) has been classified as Likely benign.
Frequency
Consequence
NM_001384900.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEMA3D | NM_001384900.1 | c.1937C>T | p.Thr646Met | missense_variant | 19/19 | ENST00000284136.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEMA3D | ENST00000284136.11 | c.1937C>T | p.Thr646Met | missense_variant | 19/19 | 5 | NM_001384900.1 | P1 | |
SEMA3D | ENST00000484038.1 | n.1063C>T | non_coding_transcript_exon_variant | 10/10 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000296 AC: 45AN: 152040Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000499 AC: 125AN: 250402Hom.: 0 AF XY: 0.000465 AC XY: 63AN XY: 135348
GnomAD4 exome AF: 0.000242 AC: 353AN: 1461082Hom.: 2 Cov.: 32 AF XY: 0.000253 AC XY: 184AN XY: 726712
GnomAD4 genome ? AF: 0.000296 AC: 45AN: 152040Hom.: 0 Cov.: 32 AF XY: 0.000296 AC XY: 22AN XY: 74260
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 27, 2021 | The c.1937C>T (p.T646M) alteration is located in exon 17 (coding exon 17) of the SEMA3D gene. This alteration results from a C to T substitution at nucleotide position 1937, causing the threonine (T) at amino acid position 646 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at