rs2474329

Variant names:

• chr10-132348013-C-A
• rs2474329
• NM_030626.3:c.583C>A

Your query was ambiguous. Multiple possible variants found:

• chr10-132348013-C-A
• chr10-132348013-C-G
• chr10-132348013-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_030626.3(LRRC27):​c.583C>A​(p.Arg195Ser) 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. R195H) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: LRRC27 NM_030626.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117
• Publications: 28 publications found

Genes affected

LRRC27 (HGNC:29346): (leucine rich repeat containing 27)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.044553667).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030626.3. 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
	LRRC27	NM_030626.3	MANE Select	c.583C>A	p.Arg195Ser	missense	Exon 6 of 11	NP_085129.1
	LRRC27	NM_001143757.2		c.583C>A	p.Arg195Ser	missense	Exon 6 of 11	NP_001137229.1
	LRRC27	NM_001143758.2		c.583C>A	p.Arg195Ser	missense	Exon 6 of 8	NP_001137230.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC27	ENST00000368614.8	TSL:1 MANE Select	c.583C>A	p.Arg195Ser	missense	Exon 6 of 11	ENSP00000357603.3
	LRRC27	ENST00000368613.8	TSL:1	c.583C>A	p.Arg195Ser	missense	Exon 6 of 11	ENSP00000357602.4
	LRRC27	ENST00000625755.2	TSL:1	c.583C>A	p.Arg195Ser	missense	Exon 6 of 8	ENSP00000486582.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 12283

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.31	T
BayesDel_noAF	Benign	-0.68
CADD	Benign	0.026
DANN	Benign	0.22
DEOGEN2	Benign	0.013	T
Eigen	Benign	-1.6
Eigen_PC	Benign	-1.6
FATHMM_MKL	Benign	0.00037	N
LIST_S2	Benign	0.50	T
M_CAP	Benign	0.0011	T
MetaRNN	Benign	0.045	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	-0.55	N
PhyloP100		-0.12
PrimateAI	Benign	0.22	T
PROVEAN	Benign	0.37	N
REVEL	Benign	0.018
Sift	Benign	0.76	T
Sift4G	Benign	0.60	T
Polyphen		0.0030	B
Vest4		0.016
MutPred		0.26		Gain of phosphorylation at R195 (P = 0.0245)
MVP		0.081
MPC		0.069
ClinPred		0.032	T
GERP RS		-0.65
Varity_R		0.063
gMVP		0.23
Mutation Taster		=98/2	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs2474329; hg19: chr10-134161517;