2-28310080-A-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PVS1_ModerateBP6_ModerateBS2
The NM_199192.3(BABAM2):c.1089-2A>C variant causes a splice acceptor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00353 in 1,614,178 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_199192.3 splice_acceptor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00288 AC: 439AN: 152256Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.00283 AC: 711AN: 251424Hom.: 4 AF XY: 0.00275 AC XY: 374AN XY: 135880
GnomAD4 exome AF: 0.00360 AC: 5264AN: 1461804Hom.: 16 Cov.: 30 AF XY: 0.00364 AC XY: 2644AN XY: 727204
GnomAD4 genome AF: 0.00288 AC: 439AN: 152374Hom.: 4 Cov.: 32 AF XY: 0.00274 AC XY: 204AN XY: 74516
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | BABAM2: BS2; ENSG00000223522: BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at