16-30489160-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_002209.3(ITGAL):c.1080+5G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000937 in 1,613,982 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_002209.3 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: 0.00502 AC: 764AN: 152170Hom.: 7 Cov.: 31
GnomAD3 exomes AF: 0.00148 AC: 371AN: 251402Hom.: 4 AF XY: 0.00114 AC XY: 155AN XY: 135876
GnomAD4 exome AF: 0.000509 AC: 744AN: 1461694Hom.: 7 Cov.: 31 AF XY: 0.000422 AC XY: 307AN XY: 727150
GnomAD4 genome AF: 0.00504 AC: 768AN: 152288Hom.: 7 Cov.: 31 AF XY: 0.00465 AC XY: 346AN XY: 74456
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Mar 29, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at