6-138908823-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001286611.2(REPS1):c.2068-7C>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 0.00185 in 1,611,020 control chromosomes in the GnomAD database, including 48 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_001286611.2 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0104 AC: 1583AN: 152170Hom.: 22 Cov.: 32
GnomAD3 exomes AF: 0.00254 AC: 630AN: 247828Hom.: 9 AF XY: 0.00183 AC XY: 245AN XY: 133896
GnomAD4 exome AF: 0.000960 AC: 1401AN: 1458732Hom.: 26 Cov.: 31 AF XY: 0.000849 AC XY: 616AN XY: 725586
GnomAD4 genome AF: 0.0104 AC: 1584AN: 152288Hom.: 22 Cov.: 32 AF XY: 0.00998 AC XY: 743AN XY: 74456
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 15, 2025 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at