NM_001370785.2:c.101-18795T>G

Variant names:

• chr1-69741396-T-G
• rs10889850
• NM_001370785.2:c.101-18795T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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 Gene-Disease associations (from GenCC):

• neurodevelopmental disorder

  Inheritance: AD Classification: STRONG Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001370785.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC7	NM_001370785.2	MANE Select	c.101-18795T>G		intron	N/A	NP_001357714.1	A0A494C1A4
	LRRC7	NM_001366838.3		c.101-18795T>G		intron	N/A	NP_001353767.1
	LRRC7	NM_001330635.3		c.2-18795T>G		intron	N/A	NP_001317564.1	A0A075B6E9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LRRC7	ENST00000651989.2	MANE Select	c.101-18795T>G		intron	N/A	ENSP00000498937.2	A0A494C1A4
	LRRC7	ENST00000370958.5	TSL:1	c.101-18795T>G		intron	N/A	ENSP00000359997.1	B1AKT2
	LRRC7	ENST00000310961.9	TSL:5	c.2-18795T>G		intron	N/A	ENSP00000309245.4	A0A075B6E9

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

African (AFR) AF: 0.779 AC: 32194 AN: 41314

American (AMR) AF: 0.740 AC: 11215 AN: 15148

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2211 AN: 3454

East Asian (EAS) AF: 0.916 AC: 4710 AN: 5142

South Asian (SAS) AF: 0.776 AC: 3733 AN: 4808

European-Finnish (FIN) AF: 0.674 AC: 7073 AN: 10498

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.677 AC: 45920 AN: 67846

Other (OTH) AF: 0.699 AC: 1468 AN: 2100

Alfa AF: 0.693 Hom.: 141839

Bravo AF: 0.731

Asia WGS AF: 0.853 AC: 2966 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.2
DANN	Benign	0.75
PhyloP100		-0.14
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10889850; hg19: chr1-70207079;