2-169259078-T-G
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004525.3(LRP2):c.2460A>C(p.Thr820Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,270 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. T820T) has been classified as Benign.
Frequency
Consequence
NM_004525.3 synonymous
Scores
Clinical Significance
Conservation
Publications
- Donnai-Barrow syndromeInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), G2P, Orphanet
- Stickler syndromeInheritance: AD Classification: MODERATE Submitted by: Genomics England PanelApp
- intellectual disabilityInheritance: AD Classification: LIMITED Submitted by: G2P
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LRP2 | NM_004525.3 | c.2460A>C | p.Thr820Thr | synonymous_variant | Exon 17 of 79 | ENST00000649046.1 | NP_004516.2 | |
LRP2 | XM_011511183.4 | c.2460A>C | p.Thr820Thr | synonymous_variant | Exon 17 of 78 | XP_011509485.1 | ||
LRP2 | XM_047444340.1 | c.1536A>C | p.Thr512Thr | synonymous_variant | Exon 17 of 79 | XP_047300296.1 | ||
LRP2 | XM_011511184.3 | c.171A>C | p.Thr57Thr | synonymous_variant | Exon 2 of 64 | XP_011509486.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRP2 | ENST00000649046.1 | c.2460A>C | p.Thr820Thr | synonymous_variant | Exon 17 of 79 | NM_004525.3 | ENSP00000496870.1 | |||
LRP2 | ENST00000443831.1 | c.2049A>C | p.Thr683Thr | synonymous_variant | Exon 15 of 23 | 2 | ENSP00000409813.1 |
Frequencies
GnomAD3 genomes Cov.: 30
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461270Hom.: 0 Cov.: 44 AF XY: 0.00000138 AC XY: 1AN XY: 726956 show subpopulations
GnomAD4 genome Cov.: 30
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at