chr17-16491849-T-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001113567.3(LRRC75A):āc.142A>Cā(p.Met48Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_001113567.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRC75A | NM_001113567.3 | c.142A>C | p.Met48Leu | missense_variant | 1/4 | ENST00000470794.2 | |
LOC124903936 | XR_007065641.1 | n.1605+4403T>G | intron_variant, non_coding_transcript_variant | ||||
LRRC75A | NM_207387.4 | c.142A>C | p.Met48Leu | missense_variant | 1/3 | ||
LRRC75A | XM_047435962.1 | c.142A>C | p.Met48Leu | missense_variant | 1/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRC75A | ENST00000470794.2 | c.142A>C | p.Met48Leu | missense_variant | 1/4 | 1 | NM_001113567.3 | P1 | |
LRRC75A | ENST00000409083.7 | c.142A>C | p.Met48Leu | missense_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1244908Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 613082
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 07, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.