1-70101505-C-G

Position:

• chr1-70101505-C-G

Variant summary

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

The NM_001370785.2(LRRC7):​c.4546-6247C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.988 in 152,296 control chromosomes in the GnomAD database, including 74,454 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 0.99 (74454 hom., cov: 31)
• Consequence: LRRC7 NM_001370785.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.85

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=-0.52).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.99 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRRC7	NM_001370785.2	c.4546-6247C>G		intron_variant		ENST00000651989.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRC7	ENST00000651989.2	c.4546-6247C>G		intron_variant			NM_001370785.2	P1
LRRC7	ENST00000415775.2	c.2284-6247C>G		intron_variant		1
LRRC7	ENST00000310961.9	c.4306-6247C>G		intron_variant		5
LRRC7	ENST00000651217.1	n.4462-6247C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.988 AC: 150402 AN: 152178 Hom.: 74390 Cov.: 31

Gnomad AFR AF: 0.998

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.997

Gnomad ASJ AF: 0.999

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.990

Gnomad FIN AF: 0.989

Gnomad MID AF: 0.994

Gnomad NFE AF: 0.992

Gnomad OTH AF: 0.990

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

GnomAD4 genome AF: 0.988 AC: 150525 AN: 152296 Hom.: 74454 Cov.: 31 AF XY: 0.987 AC XY: 73527 AN XY: 74466

Gnomad4 AFR AF: 0.998

Gnomad4 AMR AF: 0.997

Gnomad4 ASJ AF: 0.999

Gnomad4 EAS AF: 0.832

Gnomad4 SAS AF: 0.990

Gnomad4 FIN AF: 0.989

Gnomad4 NFE AF: 0.992

Gnomad4 OTH AF: 0.991

Alfa AF: 0.992 Hom.: 4044

Bravo AF: 0.988

Asia WGS AF: 0.933 AC: 3244 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	20
DANN	Benign	0.75

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: rs672961; hg19: chr1-70567188;