11-64219559-G-C
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_031471.6(FERMT3):āc.930G>Cā(p.Val310=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00162 in 1,611,558 control chromosomes in the GnomAD database, including 40 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. V310V) has been classified as Likely benign.
Frequency
Consequence
NM_031471.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FERMT3 | NM_031471.6 | c.930G>C | p.Val310= | synonymous_variant | 8/15 | ENST00000345728.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FERMT3 | ENST00000345728.10 | c.930G>C | p.Val310= | synonymous_variant | 8/15 | 1 | NM_031471.6 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00123 AC: 187AN: 152164Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00367 AC: 900AN: 245474Hom.: 14 AF XY: 0.00469 AC XY: 625AN XY: 133370
GnomAD4 exome AF: 0.00166 AC: 2422AN: 1459276Hom.: 39 Cov.: 36 AF XY: 0.00230 AC XY: 1670AN XY: 725846
GnomAD4 genome AF: 0.00123 AC: 187AN: 152282Hom.: 1 Cov.: 33 AF XY: 0.00158 AC XY: 118AN XY: 74450
ClinVar
Submissions by phenotype
Leukocyte adhesion deficiency 3 Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 08, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at