1-74470690-A-G
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001382280.1(LRRC53):āc.2932T>Cā(p.Ser978Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.653 in 400,350 control chromosomes in the GnomAD database, including 88,085 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/13 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001382280.1 missense
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LRRC53 | NM_001382280.1 | c.2932T>C | p.Ser978Pro | missense_variant | 5/5 | ENST00000294635.5 | NP_001369209.1 | |
TNNI3K | NM_015978.3 | c.2121+7140A>G | intron_variant | ENST00000326637.8 | NP_057062.1 | |||
FPGT-TNNI3K | NM_001112808.3 | c.2424+7140A>G | intron_variant | NP_001106279.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRRC53 | ENST00000294635.5 | c.2932T>C | p.Ser978Pro | missense_variant | 5/5 | 5 | NM_001382280.1 | ENSP00000294635 | P1 | |
TNNI3K | ENST00000326637.8 | c.2121+7140A>G | intron_variant | 1 | NM_015978.3 | ENSP00000322251 | P1 |
Frequencies
GnomAD3 genomes AF: 0.694 AC: 105284AN: 151810Hom.: 37900 Cov.: 31
GnomAD3 exomes AF: 0.549 AC: 201AN: 366Hom.: 58 AF XY: 0.495 AC XY: 103AN XY: 208
GnomAD4 exome AF: 0.628 AC: 155890AN: 248422Hom.: 50124 Cov.: 0 AF XY: 0.623 AC XY: 78471AN XY: 125858
GnomAD4 genome AF: 0.694 AC: 105401AN: 151928Hom.: 37961 Cov.: 31 AF XY: 0.697 AC XY: 51705AN XY: 74222
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at