rs117971741
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_014822.4(SEC24D):c.1042-6C>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00122 in 1,606,634 control chromosomes in the GnomAD database, including 43 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 Likely benign (★★).
Frequency
Consequence
NM_014822.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SEC24D | NM_014822.4 | c.1042-6C>G | splice_region_variant, intron_variant | ENST00000280551.11 | NP_055637.2 | |||
SEC24D | NM_001318066.2 | c.1045-6C>G | splice_region_variant, intron_variant | NP_001304995.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SEC24D | ENST00000280551.11 | c.1042-6C>G | splice_region_variant, intron_variant | 1 | NM_014822.4 | ENSP00000280551.6 |
Frequencies
GnomAD3 genomes AF: 0.00176 AC: 267AN: 151840Hom.: 6 Cov.: 32
GnomAD3 exomes AF: 0.00409 AC: 1001AN: 244480Hom.: 33 AF XY: 0.00376 AC XY: 497AN XY: 132022
GnomAD4 exome AF: 0.00116 AC: 1688AN: 1454708Hom.: 37 Cov.: 31 AF XY: 0.00118 AC XY: 856AN XY: 723602
GnomAD4 genome AF: 0.00174 AC: 265AN: 151926Hom.: 6 Cov.: 32 AF XY: 0.00195 AC XY: 145AN XY: 74216
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 06, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Mar 29, 2017 | - - |
SEC24D-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 21, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Cole-Carpenter syndrome 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Sep 29, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at