16-1338671-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001199097.2(BAIAP3):c.122C>T(p.Thr41Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00267 in 1,582,006 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001199097.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00242 AC: 369AN: 152182Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00287 AC: 557AN: 193810Hom.: 2 AF XY: 0.00285 AC XY: 301AN XY: 105436
GnomAD4 exome AF: 0.00270 AC: 3854AN: 1429706Hom.: 14 Cov.: 35 AF XY: 0.00277 AC XY: 1964AN XY: 708826
GnomAD4 genome AF: 0.00244 AC: 371AN: 152300Hom.: 1 Cov.: 32 AF XY: 0.00224 AC XY: 167AN XY: 74468
ClinVar
Submissions by phenotype
not provided Benign:1
BAIAP3: BS1, BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at