chr17-75843080-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_199242.3(UNC13D):c.262-7C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000261 in 1,607,498 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_199242.3 splice_region, intron
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: 0.000151 AC: 23AN: 152124Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000206 AC: 5AN: 243244Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 133226
GnomAD4 exome AF: 0.0000131 AC: 19AN: 1455256Hom.: 0 Cov.: 49 AF XY: 0.00000552 AC XY: 4AN XY: 724062
GnomAD4 genome AF: 0.000151 AC: 23AN: 152242Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74440
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Familial hemophagocytic lymphohistiocytosis 3 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 08, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at