NM_030626.3:c.160G>C

Variant names:

• chr10-132333684-G-C
• NM_030626.3:c.160G>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2 BP4_Strong BP6_Moderate

The NM_030626.3(LRRC27):​c.160G>C​(p.Glu54Gln) 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. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: LRRC27 NM_030626.3 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.168
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.022380978).
• BP6: Variant 10-132333684-G-C is Benign according to our data. Variant chr10-132333684-G-C is described in ClinVar as Likely_benign. ClinVar VariationId is 2239007.Status of the report is criteria_provided_single_submitter, 1 stars.

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.160G>C	p.Glu54Gln	missense	Exon 2 of 11	NP_085129.1	Q9C0I9-1
	LRRC27	NM_001143757.2		c.160G>C	p.Glu54Gln	missense	Exon 2 of 11	NP_001137229.1	Q9C0I9-1
	LRRC27	NM_001143758.2		c.160G>C	p.Glu54Gln	missense	Exon 2 of 8	NP_001137230.1	Q9C0I9-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC27	ENST00000368614.8	TSL:1 MANE Select	c.160G>C	p.Glu54Gln	missense	Exon 2 of 11	ENSP00000357603.3	Q9C0I9-1
	LRRC27	ENST00000368613.8	TSL:1	c.160G>C	p.Glu54Gln	missense	Exon 2 of 11	ENSP00000357602.4	Q9C0I9-1
	LRRC27	ENST00000625755.2	TSL:1	c.160G>C	p.Glu54Gln	missense	Exon 2 of 8	ENSP00000486582.1	Q9C0I9-4

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.075
BayesDel_addAF	Benign	-0.38	T
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.4
DANN	Benign	0.64
DEOGEN2	Benign	0.013	T
Eigen	Benign	-1.1
Eigen_PC	Benign	-0.94
FATHMM_MKL	Benign	0.022	N
LIST_S2	Benign	0.54	T
M_CAP	Benign	0.0014	T
MetaRNN	Benign	0.022	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	-1.4	N
PhyloP100		-0.17
PrimateAI	Benign	0.26	T
PROVEAN	Benign	0.72	N
REVEL	Benign	0.020
Sift	Benign	1.0	T
Sift4G	Benign	1.0	T
Polyphen		0.017	B
Vest4		0.075
MutPred		0.30		Loss of phosphorylation at S53 (P = 0.1136)
MVP		0.048
MPC		0.061
ClinPred		0.022	T
GERP RS		-0.13
Varity_R		0.054
gMVP		0.13
Mutation Taster		=88/12	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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

hg19: chr10-134147188;