1-69640464-G-A

Position:

• chr1-69640464-G-A

Variant summary

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

The NM_001370785.2(LRRC7):​c.3-37917G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.734 in 151,314 control chromosomes in the GnomAD database, including 41,050 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 0.73 (41050 hom., cov: 31)
• Consequence: LRRC7 NM_001370785.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRRC7	NM_001370785.2	c.3-37917G>A		intron_variant		ENST00000651989.2	NP_001357714.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LRRC7	ENST00000651989.2	c.3-37917G>A		intron_variant			NM_001370785.2	ENSP00000498937.2
LRRC7	ENST00000370958.5	c.3-37917G>A		intron_variant		1		ENSP00000359997.1
LRRC7	ENST00000310961.9	c.-174-37917G>A		intron_variant		5		ENSP00000309245.4

Frequencies

GnomAD3 genomes AF: 0.734 AC: 110916 AN: 151204 Hom.: 41022 Cov.: 31

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.799

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.673

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.734 AC: 110996 AN: 151314 Hom.: 41050 Cov.: 31 AF XY: 0.734 AC XY: 54216 AN XY: 73874

Gnomad4 AFR AF: 0.815

Gnomad4 AMR AF: 0.758

Gnomad4 ASJ AF: 0.586

Gnomad4 EAS AF: 0.639

Gnomad4 SAS AF: 0.797

Gnomad4 FIN AF: 0.694

Gnomad4 NFE AF: 0.696

Gnomad4 OTH AF: 0.716

Alfa AF: 0.734 Hom.: 5136

Bravo AF: 0.740

Asia WGS AF: 0.734 AC: 2535 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.9
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs800923; hg19: chr1-70106147;