rs373308042
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001114753.3(ENG):c.1273-4G>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 0.000064 in 1,608,404 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_001114753.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ENG | NM_001114753.3 | c.1273-4G>A | splice_region_variant, intron_variant | Intron 9 of 14 | ENST00000373203.9 | NP_001108225.1 | ||
ENG | NM_000118.4 | c.1273-4G>A | splice_region_variant, intron_variant | Intron 9 of 13 | NP_000109.1 | |||
ENG | NM_001278138.2 | c.727-4G>A | splice_region_variant, intron_variant | Intron 9 of 14 | NP_001265067.1 | |||
LOC102723566 | NR_136302.1 | n.1568+953C>T | intron_variant | Intron 4 of 5 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152198Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000676 AC: 16AN: 236788Hom.: 0 AF XY: 0.0000859 AC XY: 11AN XY: 128058
GnomAD4 exome AF: 0.0000652 AC: 95AN: 1456088Hom.: 0 Cov.: 32 AF XY: 0.0000622 AC XY: 45AN XY: 723792
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152316Hom.: 0 Cov.: 31 AF XY: 0.0000403 AC XY: 3AN XY: 74472
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2023 | ENG: BP4 - |
Hereditary hemorrhagic telangiectasia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 13, 2025 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at