X-55143826-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001166699.2(VCF2):c.304G>A(p.Glu102Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000105 in 1,206,382 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 42 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001166699.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VCF2 | NM_001166701.4 | c.*2258G>A | 3_prime_UTR_variant | Exon 3 of 3 | ENST00000685693.1 | NP_001160173.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FAM104B | ENST00000332132.8 | c.304G>A | p.Glu102Lys | missense_variant | Exon 4 of 4 | 1 | ENSP00000333394.4 | |||
FAM104B | ENST00000358460.8 | c.301G>A | p.Glu101Lys | missense_variant | Exon 4 of 4 | 1 | ENSP00000364101.3 | |||
FAM104B | ENST00000685693 | c.*2258G>A | 3_prime_UTR_variant | Exon 3 of 3 | NM_001166701.4 | ENSP00000509111.1 |
Frequencies
GnomAD3 genomes AF: 0.000503 AC: 56AN: 111337Hom.: 0 Cov.: 22 AF XY: 0.000358 AC XY: 12AN XY: 33541
GnomAD3 exomes AF: 0.000165 AC: 30AN: 182134Hom.: 0 AF XY: 0.000135 AC XY: 9AN XY: 66634
GnomAD4 exome AF: 0.0000639 AC: 70AN: 1094993Hom.: 0 Cov.: 27 AF XY: 0.0000804 AC XY: 29AN XY: 360671
GnomAD4 genome AF: 0.000512 AC: 57AN: 111389Hom.: 0 Cov.: 22 AF XY: 0.000387 AC XY: 13AN XY: 33603
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.304G>A (p.E102K) alteration is located in exon 4 (coding exon 4) of the FAM104B gene. This alteration results from a G to A substitution at nucleotide position 304, causing the glutamic acid (E) at amino acid position 102 to be replaced by a lysine (K). 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