rs3735169
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001142928.2(LRRC61):āc.428A>Gā(p.Asn143Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 1,602,884 control chromosomes in the GnomAD database, including 52,699 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 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 same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001142928.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRC61 | NM_001142928.2 | c.428A>G | p.Asn143Ser | missense_variant | 3/3 | ENST00000359623.9 | |
LRRC61 | NM_001363433.1 | c.428A>G | p.Asn143Ser | missense_variant | 3/3 | ||
LRRC61 | NM_001363434.1 | c.428A>G | p.Asn143Ser | missense_variant | 3/3 | ||
LRRC61 | NM_023942.3 | c.428A>G | p.Asn143Ser | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRC61 | ENST00000359623.9 | c.428A>G | p.Asn143Ser | missense_variant | 3/3 | 2 | NM_001142928.2 | P1 | |
LRRC61 | ENST00000323078.7 | c.428A>G | p.Asn143Ser | missense_variant | 2/2 | 1 | P1 | ||
LRRC61 | ENST00000493307.1 | c.428A>G | p.Asn143Ser | missense_variant | 4/4 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.246 AC: 37366AN: 151758Hom.: 4740 Cov.: 33
GnomAD3 exomes AF: 0.242 AC: 58797AN: 242762Hom.: 7658 AF XY: 0.248 AC XY: 32712AN XY: 131998
GnomAD4 exome AF: 0.254 AC: 369238AN: 1451006Hom.: 47965 Cov.: 36 AF XY: 0.256 AC XY: 184870AN XY: 722294
GnomAD4 genome ? AF: 0.246 AC: 37381AN: 151878Hom.: 4734 Cov.: 33 AF XY: 0.247 AC XY: 18320AN XY: 74230
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at