chr16-89816593-T-C
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP6
The NM_000135.4(FANCA):āc.23A>Gā(p.Asn8Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000341 in 1,526,774 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N8K) has been classified as Benign.
Frequency
Consequence
NM_000135.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FANCA | NM_000135.4 | c.23A>G | p.Asn8Ser | missense_variant | 1/43 | ENST00000389301.8 | |
FANCA | NM_001286167.3 | c.23A>G | p.Asn8Ser | missense_variant | 1/43 | ||
FANCA | NM_001018112.3 | c.23A>G | p.Asn8Ser | missense_variant | 1/11 | ||
FANCA | NM_001351830.2 | c.23A>G | p.Asn8Ser | missense_variant | 1/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FANCA | ENST00000389301.8 | c.23A>G | p.Asn8Ser | missense_variant | 1/43 | 1 | NM_000135.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 151956Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000323 AC: 4AN: 123836Hom.: 0 AF XY: 0.0000435 AC XY: 3AN XY: 69018
GnomAD4 exome AF: 0.0000335 AC: 46AN: 1374818Hom.: 1 Cov.: 31 AF XY: 0.0000427 AC XY: 29AN XY: 679430
GnomAD4 genome AF: 0.0000395 AC: 6AN: 151956Hom.: 0 Cov.: 34 AF XY: 0.0000404 AC XY: 3AN XY: 74244
ClinVar
Submissions by phenotype
Fanconi anemia Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 11, 2023 | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Oct 28, 2019 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden | Nov 03, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at