3-46532867-T-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_024512.5(LRRC2):āc.533A>Cā(p.Tyr178Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000919 in 1,614,010 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_024512.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRC2 | NM_024512.5 | c.533A>C | p.Tyr178Ser | missense_variant | 5/9 | ENST00000395905.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRC2 | ENST00000395905.8 | c.533A>C | p.Tyr178Ser | missense_variant | 5/9 | 1 | NM_024512.5 | P1 | |
LRRC2 | ENST00000296144.3 | c.533A>C | p.Tyr178Ser | missense_variant | 5/9 | 1 | P1 | ||
LRRC2 | ENST00000682605.1 | c.533A>C | p.Tyr178Ser | missense_variant | 5/9 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00450 AC: 685AN: 152224Hom.: 11 Cov.: 32
GnomAD3 exomes AF: 0.00128 AC: 321AN: 251276Hom.: 2 AF XY: 0.00104 AC XY: 141AN XY: 135798
GnomAD4 exome AF: 0.000545 AC: 797AN: 1461668Hom.: 1 Cov.: 33 AF XY: 0.000494 AC XY: 359AN XY: 727130
GnomAD4 genome AF: 0.00451 AC: 687AN: 152342Hom.: 11 Cov.: 32 AF XY: 0.00460 AC XY: 343AN XY: 74500
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 04, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at