chr2-96861320-A-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The ENST00000305476.10(SEMA4C):c.1808T>A(p.Phe603Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000177 in 1,607,342 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. F603L) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000305476.10 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SEMA4C | NM_017789.5 | c.1808T>A | p.Phe603Tyr | missense_variant | 15/15 | ENST00000305476.10 | NP_060259.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SEMA4C | ENST00000305476.10 | c.1808T>A | p.Phe603Tyr | missense_variant | 15/15 | 1 | NM_017789.5 | ENSP00000306844 | P1 | |
SEMA4C | ENST00000467747.1 | n.1799T>A | non_coding_transcript_exon_variant | 3/3 | 2 | |||||
SEMA4C | ENST00000474420.1 | n.1041T>A | non_coding_transcript_exon_variant | 2/2 | 2 | |||||
SEMA4C | ENST00000482925.5 | n.2198T>A | non_coding_transcript_exon_variant | 13/13 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152176Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000149 AC: 36AN: 242374Hom.: 0 AF XY: 0.000121 AC XY: 16AN XY: 132532
GnomAD4 exome AF: 0.000183 AC: 267AN: 1455048Hom.: 1 Cov.: 31 AF XY: 0.000173 AC XY: 125AN XY: 724160
GnomAD4 genome AF: 0.000118 AC: 18AN: 152294Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74466
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2023 | The c.1808T>A (p.F603Y) alteration is located in exon 15 (coding exon 14) of the SEMA4C gene. This alteration results from a T to A substitution at nucleotide position 1808, causing the phenylalanine (F) at amino acid position 603 to be replaced by a tyrosine (Y). 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