rs6733871
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_178839.5(LRRTM1):āc.989A>Gā(p.Asn330Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 1,613,676 control chromosomes in the GnomAD database, including 45,305 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_178839.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRRTM1 | ENST00000295057.4 | c.989A>G | p.Asn330Ser | missense_variant | Exon 2 of 2 | 1 | NM_178839.5 | ENSP00000295057.3 | ||
CTNNA2 | ENST00000402739.9 | c.1057-90380T>C | intron_variant | Intron 7 of 18 | 1 | NM_001282597.3 | ENSP00000384638.4 |
Frequencies
GnomAD3 genomes AF: 0.286 AC: 43417AN: 151996Hom.: 7319 Cov.: 32
GnomAD3 exomes AF: 0.267 AC: 66665AN: 250068Hom.: 10398 AF XY: 0.258 AC XY: 34992AN XY: 135372
GnomAD4 exome AF: 0.211 AC: 307823AN: 1461562Hom.: 37962 Cov.: 33 AF XY: 0.211 AC XY: 153730AN XY: 727078
GnomAD4 genome AF: 0.286 AC: 43497AN: 152114Hom.: 7343 Cov.: 32 AF XY: 0.290 AC XY: 21560AN XY: 74370
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at