rs7645635
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001375462.1(LPP):āc.1036T>Cā(p.Tyr346His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0339 in 1,613,912 control chromosomes in the GnomAD database, including 14,298 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001375462.1 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LPP | NM_001375462.1 | c.1036T>C | p.Tyr346His | missense_variant | 7/12 | ENST00000617246.5 | NP_001362391.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LPP | ENST00000617246.5 | c.1036T>C | p.Tyr346His | missense_variant | 7/12 | 1 | NM_001375462.1 | ENSP00000478901.1 |
Frequencies
GnomAD3 genomes AF: 0.174 AC: 26387AN: 151982Hom.: 7500 Cov.: 32
GnomAD3 exomes AF: 0.0469 AC: 11685AN: 249002Hom.: 3069 AF XY: 0.0351 AC XY: 4736AN XY: 134970
GnomAD4 exome AF: 0.0193 AC: 28261AN: 1461812Hom.: 6777 Cov.: 34 AF XY: 0.0169 AC XY: 12301AN XY: 727202
GnomAD4 genome AF: 0.174 AC: 26449AN: 152100Hom.: 7521 Cov.: 32 AF XY: 0.166 AC XY: 12384AN XY: 74388
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 09, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at