rs11231726
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000279227.10(FERMT3):c.1080-12C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 1,613,730 control chromosomes in the GnomAD database, including 19,072 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). There are indicators that this mutation may affect the branch point..
Frequency
Consequence
ENST00000279227.10 splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FERMT3 | NM_031471.6 | c.1080-24C>T | intron_variant | ENST00000345728.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FERMT3 | ENST00000345728.10 | c.1080-24C>T | intron_variant | 1 | NM_031471.6 | P4 |
Frequencies
GnomAD3 genomes AF: 0.111 AC: 16842AN: 152046Hom.: 1164 Cov.: 32
GnomAD3 exomes AF: 0.118 AC: 29489AN: 250840Hom.: 2003 AF XY: 0.119 AC XY: 16151AN XY: 135724
GnomAD4 exome AF: 0.151 AC: 221350AN: 1461566Hom.: 17908 Cov.: 37 AF XY: 0.149 AC XY: 108381AN XY: 727090
GnomAD4 genome AF: 0.111 AC: 16849AN: 152164Hom.: 1164 Cov.: 32 AF XY: 0.108 AC XY: 8010AN XY: 74384
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 11, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at