rs141128234
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_000135.4(FANCA):c.3792C>T(p.Ser1264=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000049 in 1,613,504 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. S1264S) has been classified as Likely benign.
Frequency
Consequence
NM_000135.4 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FANCA | NM_000135.4 | c.3792C>T | p.Ser1264= | synonymous_variant | 38/43 | ENST00000389301.8 | |
ZNF276 | NM_001113525.2 | c.*2594G>A | 3_prime_UTR_variant | 11/11 | ENST00000443381.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FANCA | ENST00000389301.8 | c.3792C>T | p.Ser1264= | synonymous_variant | 38/43 | 1 | NM_000135.4 | P1 | |
ZNF276 | ENST00000443381.7 | c.*2594G>A | 3_prime_UTR_variant | 11/11 | 1 | NM_001113525.2 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000263 AC: 40AN: 152034Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000559 AC: 14AN: 250666Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135542
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1461352Hom.: 0 Cov.: 31 AF XY: 0.0000220 AC XY: 16AN XY: 726936
GnomAD4 genome AF: 0.000263 AC: 40AN: 152152Hom.: 0 Cov.: 32 AF XY: 0.000255 AC XY: 19AN XY: 74372
ClinVar
Submissions by phenotype
Fanconi anemia Benign:2
Likely benign, criteria provided, single submitter | curation | Sema4, Sema4 | Sep 20, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 02, 2023 | - - |
FANCA-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 13, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at