11-1840461-G-C
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_003282.4(TNNI2):c.57+17G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000465 in 1,608,362 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_003282.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TNNI2 | NM_003282.4 | c.57+17G>C | intron_variant | Intron 4 of 7 | ENST00000381911.6 | NP_003273.1 | ||
TNNI2 | NM_001145829.2 | c.57+17G>C | intron_variant | Intron 4 of 7 | NP_001139301.1 | |||
TNNI2 | NM_001145841.2 | c.57+17G>C | intron_variant | Intron 2 of 5 | NP_001139313.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000486 AC: 74AN: 152172Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000478 AC: 112AN: 234122Hom.: 0 AF XY: 0.000434 AC XY: 56AN XY: 128900
GnomAD4 exome AF: 0.000464 AC: 675AN: 1456070Hom.: 1 Cov.: 35 AF XY: 0.000429 AC XY: 311AN XY: 724292
GnomAD4 genome AF: 0.000479 AC: 73AN: 152292Hom.: 0 Cov.: 33 AF XY: 0.000443 AC XY: 33AN XY: 74468
ClinVar
Submissions by phenotype
not specified Benign:2
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at