chr4-20253997-G-A
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1
The NM_004787.4(SLIT2):c.179+3G>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 0.0185 in 1,600,262 control chromosomes in the GnomAD database, including 700 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 Benign (★★).
Frequency
Consequence
NM_004787.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0146 AC: 2221AN: 152022Hom.: 33 Cov.: 32
GnomAD3 exomes AF: 0.0234 AC: 5670AN: 241792Hom.: 212 AF XY: 0.0274 AC XY: 3602AN XY: 131324
GnomAD4 exome AF: 0.0189 AC: 27424AN: 1448124Hom.: 667 Cov.: 32 AF XY: 0.0213 AC XY: 15311AN XY: 720326
GnomAD4 genome AF: 0.0146 AC: 2224AN: 152138Hom.: 33 Cov.: 32 AF XY: 0.0157 AC XY: 1168AN XY: 74372
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 28, 2025 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at