rs757588678

Variant names:

• chr10-70323872-C-G
• rs757588678
• NM_001278212.2:c.391G>C

Your query was ambiguous. Multiple possible variants found:

• chr10-70323872-C-G
• chr10-70323872-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001278212.2(LRRC20):​c.391G>C​(p.Glu131Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/22 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 variant affecting the same amino acid position, but resulting in a different missense (i.e. E131G) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: LRRC20 NM_001278212.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.42
• Publications: 0 publications found

Genes affected

LRRC20 (HGNC:23421): (leucine rich repeat containing 20)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.077415586).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001278212.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC20	NM_001278212.2	MANE Select	c.391G>C	p.Glu131Gln	missense	Exon 4 of 5	NP_001265141.1	Q8TCA0-1
	LRRC20	NM_001278211.2		c.391G>C	p.Glu131Gln	missense	Exon 4 of 5	NP_001265140.1	Q8TCA0-1
	LRRC20	NM_207119.3		c.391G>C	p.Glu131Gln	missense	Exon 4 of 5	NP_997002.1	Q8TCA0-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC20	ENST00000446961.4	TSL:2 MANE Select	c.391G>C	p.Glu131Gln	missense	Exon 4 of 5	ENSP00000413745.2	Q8TCA0-1
	LRRC20	ENST00000355790.8	TSL:1	c.391G>C	p.Glu131Gln	missense	Exon 4 of 5	ENSP00000348043.4	Q8TCA0-1
	LRRC20	ENST00000373224.5	TSL:2	c.391G>C	p.Glu131Gln	missense	Exon 4 of 5	ENSP00000362321.1	Q8TCA0-1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.076
BayesDel_addAF	Benign	-0.14	T
BayesDel_noAF	Benign	-0.44
CADD	Benign	16
DANN	Benign	0.83
DEOGEN2	Benign	0.0017	T
Eigen	Benign	-0.78
Eigen_PC	Benign	-0.57
FATHMM_MKL	Benign	0.69	D
LIST_S2	Benign	0.83	T
M_CAP	Benign	0.0087	T
MetaRNN	Benign	0.077	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	-1.0	N
PhyloP100		1.4
PrimateAI	Uncertain	0.50	T
PROVEAN	Benign	0.18	N
REVEL	Benign	0.026
Sift	Benign	0.59	T
Sift4G	Benign	0.21	T
Polyphen		0.0020	B
Vest4		0.34
MutPred		0.36		Gain of sheet (P = 0.0827)
MVP		0.56
MPC		0.64
ClinPred		0.67	D
GERP RS		3.2
Varity_R		0.080
gMVP		0.36
Mutation Taster		=88/12	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs757588678; hg19: chr10-72083628;