chr1-69741396-T-G

Position:

• chr1-69741396-T-G

Variant summary

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

The NM_001370785.2(LRRC7):​c.101-18795T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.721 in 151,514 control chromosomes in the GnomAD database, including 39,778 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 0.72 (39778 hom., cov: 29)
• Consequence: LRRC7 NM_001370785.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRRC7	NM_001370785.2	c.101-18795T>G		intron_variant		ENST00000651989.2	NP_001357714.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LRRC7	ENST00000651989.2	c.101-18795T>G		intron_variant			NM_001370785.2	ENSP00000498937	P1
LRRC7	ENST00000370958.5	c.101-18795T>G		intron_variant		1		ENSP00000359997
LRRC7	ENST00000310961.9	c.2-18795T>G		intron_variant		5		ENSP00000309245

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109237 AN: 151396 Hom.: 39761 Cov.: 29

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.916

Gnomad SAS AF: 0.778

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.695

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

GnomAD4 genome AF: 0.721 AC: 109299 AN: 151514 Hom.: 39778 Cov.: 29 AF XY: 0.725 AC XY: 53630 AN XY: 73982

Gnomad4 AFR AF: 0.779

Gnomad4 AMR AF: 0.740

Gnomad4 ASJ AF: 0.640

Gnomad4 EAS AF: 0.916

Gnomad4 SAS AF: 0.776

Gnomad4 FIN AF: 0.674

Gnomad4 NFE AF: 0.677

Gnomad4 OTH AF: 0.699

Alfa AF: 0.684 Hom.: 67786

Bravo AF: 0.731

Asia WGS AF: 0.853 AC: 2966 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.2
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10889850; hg19: chr1-70207079;