chr17-4539896-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_014520.4(MYBBP1A):c.3506G>A(p.Arg1169Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000749 in 1,601,380 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_014520.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYBBP1A | NM_014520.4 | c.3506G>A | p.Arg1169Gln | missense_variant | 26/26 | ENST00000254718.9 | |
MYBBP1A | NM_001105538.2 | c.3506G>A | p.Arg1169Gln | missense_variant | 26/27 | ||
MYBBP1A | XM_011523616.3 | c.2750G>A | p.Arg917Gln | missense_variant | 21/21 | ||
MYBBP1A | XM_024450536.2 | c.*6G>A | 3_prime_UTR_variant | 25/25 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYBBP1A | ENST00000254718.9 | c.3506G>A | p.Arg1169Gln | missense_variant | 26/26 | 1 | NM_014520.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152096Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000140 AC: 34AN: 242272Hom.: 0 AF XY: 0.000121 AC XY: 16AN XY: 131750
GnomAD4 exome AF: 0.0000773 AC: 112AN: 1449284Hom.: 0 Cov.: 36 AF XY: 0.0000749 AC XY: 54AN XY: 721424
GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 152096Hom.: 0 Cov.: 31 AF XY: 0.0000404 AC XY: 3AN XY: 74294
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 24, 2023 | The c.3506G>A (p.R1169Q) alteration is located in exon 26 (coding exon 26) of the MYBBP1A gene. This alteration results from a G to A substitution at nucleotide position 3506, causing the arginine (R) at amino acid position 1169 to be replaced by a glutamine (Q). 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