7-150337498-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001142928.2(LRRC61):c.637A>G(p.Ser213Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000293 in 1,602,838 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001142928.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRC61 | NM_001142928.2 | c.637A>G | p.Ser213Gly | missense_variant | 3/3 | ENST00000359623.9 | |
LRRC61 | NM_001363433.1 | c.637A>G | p.Ser213Gly | missense_variant | 3/3 | ||
LRRC61 | NM_001363434.1 | c.637A>G | p.Ser213Gly | missense_variant | 3/3 | ||
LRRC61 | NM_023942.3 | c.637A>G | p.Ser213Gly | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRC61 | ENST00000359623.9 | c.637A>G | p.Ser213Gly | missense_variant | 3/3 | 2 | NM_001142928.2 | P1 | |
LRRC61 | ENST00000323078.7 | c.637A>G | p.Ser213Gly | missense_variant | 2/2 | 1 | P1 | ||
ENST00000647589.1 | n.16A>G | non_coding_transcript_exon_variant | 1/2 | ||||||
LRRC61 | ENST00000493307.1 | c.637A>G | p.Ser213Gly | missense_variant | 4/4 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152174Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000211 AC: 5AN: 237322Hom.: 0 AF XY: 0.0000231 AC XY: 3AN XY: 129884
GnomAD4 exome AF: 0.0000262 AC: 38AN: 1450664Hom.: 0 Cov.: 32 AF XY: 0.0000277 AC XY: 20AN XY: 721954
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152174Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 14, 2023 | The c.637A>G (p.S213G) alteration is located in exon 3 (coding exon 1) of the LRRC61 gene. This alteration results from a A to G substitution at nucleotide position 637, causing the serine (S) at amino acid position 213 to be replaced by a glycine (G). 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