chr4-145514438-G-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The NM_005900.3(SMAD1):c.-176G>A variant causes a splice region, 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00301 in 559,914 control chromosomes in the GnomAD database, including 28 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_005900.3 splice_region, 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMAD1 | NM_005900.3 | c.-176G>A | splice_region_variant, 5_prime_UTR_variant | 2/7 | ENST00000302085.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMAD1 | ENST00000302085.9 | c.-176G>A | splice_region_variant, 5_prime_UTR_variant | 2/7 | 1 | NM_005900.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00836 AC: 1271AN: 152046Hom.: 26 Cov.: 32
GnomAD4 exome AF: 0.00102 AC: 414AN: 407750Hom.: 2 Cov.: 5 AF XY: 0.000914 AC XY: 192AN XY: 210134
GnomAD4 genome ? AF: 0.00837 AC: 1273AN: 152164Hom.: 26 Cov.: 32 AF XY: 0.00765 AC XY: 569AN XY: 74378
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 12, 2022 | See Variant Classification Assertion Criteria. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at