1-74489191-A-G
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_015978.3(TNNI3K):c.2124A>G(p.Gly708=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000428 in 1,610,756 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_015978.3 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNNI3K | NM_015978.3 | c.2124A>G | p.Gly708= | splice_region_variant, synonymous_variant | 22/25 | ENST00000326637.8 | |
FPGT-TNNI3K | NM_001112808.3 | c.2427A>G | p.Gly809= | splice_region_variant, synonymous_variant | 24/27 | ||
LRRC53 | NM_001382280.1 | c.-26-5816T>C | intron_variant | ENST00000294635.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNNI3K | ENST00000326637.8 | c.2124A>G | p.Gly708= | splice_region_variant, synonymous_variant | 22/25 | 1 | NM_015978.3 | P1 | |
LRRC53 | ENST00000294635.5 | c.-26-5816T>C | intron_variant | 5 | NM_001382280.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 248528Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134420
GnomAD4 exome AF: 0.0000439 AC: 64AN: 1458588Hom.: 0 Cov.: 30 AF XY: 0.0000427 AC XY: 31AN XY: 725588
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74340
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 13, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at