1-70023183-G-T

Position:

• chr1-70023183-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2 PP2 BP4_Moderate

The NM_001370785.2(LRRC7):​c.1603G>T​(p.Ala535Ser) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: LRRC7 NM_001370785.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 4.53

Genes affected

LRRC7 (HGNC:18531): (leucine rich repeat containing 7) Predicted to be involved in several processes, including establishment or maintenance of epithelial cell apical/basal polarity; positive regulation of neuron projection development; and receptor clustering. Located in several cellular components, including centrosome; cytosol; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

LRRC7-AS1 (HGNC:40843): (LRRC7 antisense RNA 1)

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant where missense usually causes diseases, LRRC7
• BP4: Computational evidence support a benign effect (MetaRNN=0.2564602).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRRC7	NM_001370785.2	c.1603G>T	p.Ala535Ser	missense_variant	17/27	ENST00000651989.2
LRRC7-AS1	XR_001738107.2	n.4709-785C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRC7	ENST00000651989.2	c.1603G>T	p.Ala535Ser	missense_variant	17/27		NM_001370785.2	P1
LRRC7-AS1	ENST00000414132.5	n.92-785C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Dec 27, 2022

The c.1489G>T (p.A497S) alteration is located in exon 15 (coding exon 15) of the LRRC7 gene. This alteration results from a G to T substitution at nucleotide position 1489, causing the alanine (A) at amino acid position 497 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.11	T
BayesDel_noAF	Benign	-0.40
CADD	Benign	21
DANN	Benign	0.96
DEOGEN2	Benign	0.010	T;T
Eigen	Benign	-0.18
Eigen_PC	Benign	0.088
FATHMM_MKL	Uncertain	0.86	D
LIST_S2	Benign	0.86	D;D
M_CAP	Benign	0.0027	T
MetaRNN	Benign	0.26	T;T
MetaSVM	Benign	-1.0	T
MutationTaster	Benign	0.59	D;D
PrimateAI	Uncertain	0.65	T
PROVEAN	Benign	0.090	N;N
REVEL	Benign	0.083
Sift	Benign	0.25	T;T
Polyphen		0.039	.;B
Vest4		0.52
MutPred		0.42		.;Gain of disorder (P = 0.0522);
MVP		0.43
MPC		0.21
ClinPred		0.46	T
GERP RS		5.9
Varity_R		0.13
gMVP		0.16

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-70488866; COSMIC: COSV99230390; COSMIC: COSV99230390;