4-99342788-A-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_000669.5(ADH1C):c.828+7T>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 0.00282 in 1,610,326 control chromosomes in the GnomAD database, including 16 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_000669.5 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ADH1C | NM_000669.5 | c.828+7T>A | splice_region_variant, intron_variant | ENST00000515683.6 | NP_000660.1 | |||
ADH1C | NR_133005.2 | n.855+51T>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADH1C | ENST00000515683.6 | c.828+7T>A | splice_region_variant, intron_variant | 1 | NM_000669.5 | ENSP00000426083 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00285 AC: 434AN: 152242Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.00169 AC: 424AN: 250476Hom.: 2 AF XY: 0.00172 AC XY: 233AN XY: 135416
GnomAD4 exome AF: 0.00282 AC: 4111AN: 1457966Hom.: 14 Cov.: 70 AF XY: 0.00273 AC XY: 1983AN XY: 725396
GnomAD4 genome AF: 0.00285 AC: 434AN: 152360Hom.: 2 Cov.: 33 AF XY: 0.00250 AC XY: 186AN XY: 74510
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2022 | ADH1C: BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at