7-1470931-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_001080453.3(INTS1):c.6372G>A(p.Thr2124Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000019 in 1,576,930 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_001080453.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
INTS1 | ENST00000404767.8 | c.6372G>A | p.Thr2124Thr | synonymous_variant | Exon 47 of 48 | 5 | NM_001080453.3 | ENSP00000385722.3 | ||
INTS1 | ENST00000493446.1 | n.356G>A | non_coding_transcript_exon_variant | Exon 5 of 6 | 3 | |||||
INTS1 | ENST00000483196.1 | c.*202G>A | downstream_gene_variant | 5 | ENSP00000419206.1 | |||||
INTS1 | ENST00000479671.1 | n.*240G>A | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000321 AC: 6AN: 187114Hom.: 0 AF XY: 0.0000396 AC XY: 4AN XY: 100994
GnomAD4 exome AF: 0.0000204 AC: 29AN: 1424714Hom.: 0 Cov.: 31 AF XY: 0.0000241 AC XY: 17AN XY: 705464
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74362
ClinVar
Submissions by phenotype
INTS1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at