rs3749350
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_020873.7(LRRN1):c.396C>A(p.Thr132=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 1,613,828 control chromosomes in the GnomAD database, including 24,228 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. T132T) has been classified as Benign.
Frequency
Consequence
NM_020873.7 synonymous
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 |
---|---|---|---|---|---|---|---|
LRRN1 | NM_020873.7 | c.396C>A | p.Thr132= | synonymous_variant | 2/2 | ENST00000319331.4 | |
LRRN1 | NM_001324188.2 | c.396C>A | p.Thr132= | synonymous_variant | 3/3 | ||
LRRN1 | NM_001324189.2 | c.396C>A | p.Thr132= | synonymous_variant | 3/3 | ||
LRRN1 | XM_047448644.1 | c.396C>A | p.Thr132= | synonymous_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRN1 | ENST00000319331.4 | c.396C>A | p.Thr132= | synonymous_variant | 2/2 | 1 | NM_020873.7 | P1 | |
SUMF1 | ENST00000448413.5 | c.1192-17528G>T | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.211 AC: 32004AN: 151928Hom.: 4287 Cov.: 32
GnomAD3 exomes AF: 0.188 AC: 47269AN: 251112Hom.: 5791 AF XY: 0.181 AC XY: 24612AN XY: 135726
GnomAD4 exome AF: 0.150 AC: 219014AN: 1461782Hom.: 19927 Cov.: 75 AF XY: 0.150 AC XY: 109267AN XY: 727212
GnomAD4 genome AF: 0.211 AC: 32063AN: 152046Hom.: 4301 Cov.: 32 AF XY: 0.212 AC XY: 15790AN XY: 74336
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at