Variant chr8-91189566-A-C 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_001129890.2(LRRC69):c.696A>C(p.Pro232=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00921 in 1,551,128 control chromosomes in the GnomAD database, including 115 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0084 ( 11 hom., cov: 32)

Exomes 𝑓: 0.0093 ( 104 hom. )

Consequence

LRRC69
NM_001129890.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0230

Variant links:

Genes affected

LRRC69 (HGNC:34303): (leucine rich repeat containing 69) Predicted to be involved in signal transduction. [provided by Alliance of Genome Resources, Apr 2022]

LRRC69 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP6

Variant 8-91189566-A-C is Benign according to our data. Variant chr8-91189566-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 2658686.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.023 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 11 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
LRRC69	NM_001129890.2 linkuse as main transcript	c.696A>C	p.Pro232=	synonymous_variant	6/8	ENST00000448384.3	NP_001123362.1
LRRC69	NM_001354470.2 linkuse as main transcript	c.228A>C	p.Pro76=	synonymous_variant	2/4		NP_001341399.1
LRRC69	NR_148895.2 linkuse as main transcript	n.1138A>C		non_coding_transcript_exon_variant	8/11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LRRC69	ENST00000448384.3 linkuse as main transcript	c.696A>C	p.Pro232=	synonymous_variant	6/8	5	NM_001129890.2	ENSP00000400803	P1	Q6ZNQ3-1
LRRC69	ENST00000343709.7 linkuse as main transcript	c.228A>C	p.Pro76=	synonymous_variant	2/4	2		ENSP00000343221		Q6ZNQ3-2
LRRC69	ENST00000520099.5 linkuse as main transcript	c.*885A>C		3_prime_UTR_variant, NMD_transcript_variant	8/11	2		ENSP00000428537

Frequencies

GnomAD3 genomes

AF:

0.00844

AC:

1285

AN:

152180

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00145

Gnomad AMI

AF:

0.00768

Gnomad AMR

AF:

0.00262

Gnomad ASJ

AF:

0.00490

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00145

Gnomad FIN

AF:

0.0423

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0102

Gnomad OTH

AF:

0.00431

GnomAD3 exomes

AF:

0.00924

AC:

1452

AN:

157152

Hom.:

AF XY:

0.00888

AC XY:

738

AN XY:

83144

show subpopulations

Gnomad AFR exome

AF:

0.000871

Gnomad AMR exome

AF:

0.00231

Gnomad ASJ exome

AF:

0.00599

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00351

Gnomad FIN exome

AF:

0.0390

Gnomad NFE exome

AF:

0.00942

Gnomad OTH exome

AF:

0.00590

GnomAD4 exome

AF:

0.00929

AC:

13002

AN:

1398830

Hom.:

104

Cov.:

AF XY:

0.00912

AC XY:

6290

AN XY:

689916

show subpopulations

Gnomad4 AFR exome

AF:

0.00104

Gnomad4 AMR exome

AF:

0.00230

Gnomad4 ASJ exome

AF:

0.00588

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00337

Gnomad4 FIN exome

AF:

0.0365

Gnomad4 NFE exome

AF:

0.00956

Gnomad4 OTH exome

AF:

0.00611

GnomAD4 genome

AF:

0.00844

AC:

1285

AN:

152298

Hom.:

Cov.:

AF XY:

0.00959

AC XY:

714

AN XY:

74468

show subpopulations

Gnomad4 AFR

AF:

0.00144

Gnomad4 AMR

AF:

0.00261

Gnomad4 ASJ

AF:

0.00490

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00145

Gnomad4 FIN

AF:

0.0423

Gnomad4 NFE

AF:

0.0102

Gnomad4 OTH

AF:

0.00427

Alfa

AF:

0.00834

Hom.:

Bravo

AF:

0.00507

Asia WGS

AF:

0.000866

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

Apr 01, 2023

LRRC69: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

6.7

DANN

Benign

0.78

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

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