chr17-64859887-T-C
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM2PP2BP4_Strong
The NM_199340.5(LRRC37A3):c.4259A>G(p.Asn1420Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,613,310 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N1420D) has been classified as Uncertain significance.
Frequency
Consequence
NM_199340.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRC37A3 | NM_199340.5 | c.4259A>G | p.Asn1420Ser | missense_variant | 12/15 | ENST00000584306.6 | |
LOC105376844 | XR_934912.4 | n.177+9900T>C | intron_variant, non_coding_transcript_variant | ||||
LRRC37A3 | NM_001303255.3 | c.1613A>G | p.Asn538Ser | missense_variant | 8/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRC37A3 | ENST00000584306.6 | c.4259A>G | p.Asn1420Ser | missense_variant | 12/15 | 1 | NM_199340.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152066Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000805 AC: 2AN: 248536Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134774
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461244Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 726942
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152066Hom.: 0 Cov.: 31 AF XY: 0.0000404 AC XY: 3AN XY: 74270
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 02, 2023 | The c.4259A>G (p.N1420S) alteration is located in exon 11 (coding exon 9) of the LRRC37A3 gene. This alteration results from a A to G substitution at nucleotide position 4259, causing the asparagine (N) at amino acid position 1420 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at