chr17-64860035-G-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 1P and 14B. PP2BP4_StrongBP6_ModerateBA1
The NM_199340.5(LRRC37A3):c.4111C>T(p.Pro1371Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00276 in 1,613,886 control chromosomes in the GnomAD database, including 101 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. P1371P) has been classified as Benign.
Frequency
Consequence
NM_199340.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRC37A3 | NM_199340.5 | c.4111C>T | p.Pro1371Ser | missense_variant | 12/15 | ENST00000584306.6 | |
LOC105376844 | XR_934912.4 | n.177+10048G>A | intron_variant, non_coding_transcript_variant | ||||
LRRC37A3 | NM_001303255.3 | c.1465C>T | p.Pro489Ser | missense_variant | 8/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRC37A3 | ENST00000584306.6 | c.4111C>T | p.Pro1371Ser | missense_variant | 12/15 | 1 | NM_199340.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0146 AC: 2221AN: 152116Hom.: 51 Cov.: 31
GnomAD3 exomes AF: 0.00387 AC: 962AN: 248872Hom.: 27 AF XY: 0.00291 AC XY: 393AN XY: 135066
GnomAD4 exome AF: 0.00153 AC: 2238AN: 1461652Hom.: 50 Cov.: 33 AF XY: 0.00127 AC XY: 924AN XY: 727136
GnomAD4 genome ? AF: 0.0146 AC: 2224AN: 152234Hom.: 51 Cov.: 31 AF XY: 0.0141 AC XY: 1050AN XY: 74444
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at