rs7521532

chr1-70112935-G-Achr1-70112935-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001370785.2(LRRC7):c.4620+5109G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,048 control chromosomes in the GnomAD database, including 1,736 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.13 (1736 hom., cov: 32)
• Consequence: LRRC7 NM_001370785.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.248

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRRC7	NM_001370785.2	c.4620+5109G>A		intron_variant		ENST00000651989.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRC7	ENST00000651989.2	c.4620+5109G>A		intron_variant			NM_001370785.2	P1

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19450 AN: 151930 Hom.: 1722 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.0937

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.0270

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.0739

Gnomad OTH AF: 0.122

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.128 AC: 19507 AN: 152048 Hom.: 1736 Cov.: 32 AF XY: 0.128 AC XY: 9486 AN XY: 74362

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.0937

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.0270

Gnomad4 NFE AF: 0.0739

Gnomad4 OTH AF: 0.122

Alfa AF: 0.0982 Hom.: 482

Bravo AF: 0.138

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.0
Dann	Benign	0.70

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

LitVar

Other links and lift over

dbSNP: rs7521532; hg19: chr1-70578618;