Variant 1-69678414-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001370785.2(LRRC7):c.36G>A(p.Pro12Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00467 in 1,603,404 control chromosomes in the GnomAD database, including 27 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0034 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0048 ( 24 hom. )

Consequence

LRRC7
NM_001370785.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.34

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.62).

BP6

Variant 1-69678414-G-A is Benign according to our data. Variant chr1-69678414-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2638874.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.35 with no splicing effect.

BS2

High AC in GnomAd4 at 516 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRRC7	NM_001370785.2 linkuse as main transcript	c.36G>A	p.Pro12Pro	synonymous_variant	2/27	ENST00000651989.2	NP_001357714.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
LRRC7	ENST00000651989.2 linkuse as main transcript	c.36G>A	p.Pro12Pro	synonymous_variant	2/27		NM_001370785.2	ENSP00000498937.2	A0A494C1A4
LRRC7	ENST00000370958.5 linkuse as main transcript	c.36G>A	p.Pro12Pro	synonymous_variant	2/8	1		ENSP00000359997.1	B1AKT2
LRRC7	ENST00000310961 linkuse as main transcript	c.-141G>A		5_prime_UTR_variant	2/27	5		ENSP00000309245.4	A0A075B6E9

Frequencies

GnomAD3 genomes

AF:

0.00340

AC:

517

AN:

151956

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000822

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.00164

Gnomad ASJ

AF:

0.000577

Gnomad EAS

AF:

0.00598

Gnomad SAS

AF:

0.00145

Gnomad FIN

AF:

0.00160

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00577

Gnomad OTH

AF:

0.00288

GnomAD3 exomes

AF:

0.00387

AC:

884

AN:

228704

Hom.:

AF XY:

0.00399

AC XY:

498

AN XY:

124962

show subpopulations

Gnomad AFR exome

AF:

0.00128

Gnomad AMR exome

AF:

0.00103

Gnomad ASJ exome

AF:

0.00125

Gnomad EAS exome

AF:

0.00649

Gnomad SAS exome

AF:

0.00189

Gnomad FIN exome

AF:

0.00219

Gnomad NFE exome

AF:

0.00586

Gnomad OTH exome

AF:

0.00353

GnomAD4 exome

AF:

0.00480

AC:

6964

AN:

1451330

Hom.:

Cov.:

AF XY:

0.00474

AC XY:

3420

AN XY:

720926

show subpopulations

Gnomad4 AFR exome

AF:

0.000751

Gnomad4 AMR exome

AF:

0.00112

Gnomad4 ASJ exome

AF:

0.00104

Gnomad4 EAS exome

AF:

0.00568

Gnomad4 SAS exome

AF:

0.00180

Gnomad4 FIN exome

AF:

0.00227

Gnomad4 NFE exome

AF:

0.00552

Gnomad4 OTH exome

AF:

0.00415

GnomAD4 genome

AF:

0.00339

AC:

516

AN:

152074

Hom.:

Cov.:

AF XY:

0.00307

AC XY:

228

AN XY:

74312

show subpopulations

Gnomad4 AFR

AF:

0.000819

Gnomad4 AMR

AF:

0.00164

Gnomad4 ASJ

AF:

0.000577

Gnomad4 EAS

AF:

0.00600

Gnomad4 SAS

AF:

0.00146

Gnomad4 FIN

AF:

0.00160

Gnomad4 NFE

AF:

0.00575

Gnomad4 OTH

AF:

0.00285

Alfa

AF:

0.00476

Hom.:

Bravo

AF:

0.00335

Asia WGS

AF:

0.00318

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Dec 01, 2022

LRRC7: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

6.2

DANN

Benign

0.65

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over