Variant 3-26710245-C-T 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_052953.4(LRRC3B):c.573C>T(p.Asp191=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00708 in 1,613,712 control chromosomes in the GnomAD database, including 61 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0062 ( 7 hom., cov: 33)

Exomes 𝑓: 0.0072 ( 54 hom. )

Consequence

LRRC3B
NM_052953.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.496

Variant links:

Genes affected

LRRC3B (HGNC:28105): (leucine rich repeat containing 3B) The protein encoded by this gene is a tumor suppressor, with lowered expression levels found in gastric, renal, colorectal, lung, and breast cancer tissues. The promoter of this gene is frequently hypermethylated in these cancer tissues, although the hypermethylation does not appear to be the cause of the reduced expression of this gene. Several transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Dec 2015]

LRRC3B 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=-0.48).

BP6

Variant 3-26710245-C-T is Benign according to our data. Variant chr3-26710245-C-T is described in ClinVar as [Benign]. Clinvar id is 774296.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.496 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 7 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRRC3B	NM_052953.4 linkuse as main transcript	c.573C>T	p.Asp191=	synonymous_variant	2/2	ENST00000396641.7	NP_443185.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
LRRC3B	ENST00000396641.7 linkuse as main transcript	c.573C>T	p.Asp191=	synonymous_variant	2/2	1	NM_052953.4	ENSP00000379880	P1
LRRC3B	ENST00000417744.5 linkuse as main transcript	c.573C>T	p.Asp191=	synonymous_variant	3/3	1		ENSP00000406370	P1
LRRC3B	ENST00000456208.2 linkuse as main transcript	c.573C>T	p.Asp191=	synonymous_variant	3/3	1		ENSP00000394940	P1
LRRC3B	ENST00000648296.1 linkuse as main transcript	c.573C>T	p.Asp191=	synonymous_variant, NMD_transcript_variant	3/5			ENSP00000497471

Frequencies

GnomAD3 genomes

AF:

0.00620

AC:

943

AN:

152152

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00130

Gnomad AMI

AF:

0.0186

Gnomad AMR

AF:

0.00596

Gnomad ASJ

AF:

0.0141

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00103

Gnomad FIN

AF:

0.0167

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.00779

Gnomad OTH

AF:

0.00717

GnomAD3 exomes

AF:

0.00624

AC:

1558

AN:

249524

Hom.:

AF XY:

0.00614

AC XY:

828

AN XY:

134920

show subpopulations

Gnomad AFR exome

AF:

0.00173

Gnomad AMR exome

AF:

0.00412

Gnomad ASJ exome

AF:

0.0106

Gnomad EAS exome

AF:

0.000110

Gnomad SAS exome

AF:

0.000786

Gnomad FIN exome

AF:

0.0164

Gnomad NFE exome

AF:

0.00764

Gnomad OTH exome

AF:

0.00741

GnomAD4 exome

AF:

0.00717

AC:

10478

AN:

1461442

Hom.:

Cov.:

AF XY:

0.00705

AC XY:

5129

AN XY:

727018

show subpopulations

Gnomad4 AFR exome

AF:

0.00170

Gnomad4 AMR exome

AF:

0.00470

Gnomad4 ASJ exome

AF:

0.0111

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00111

Gnomad4 FIN exome

AF:

0.0175

Gnomad4 NFE exome

AF:

0.00756

Gnomad4 OTH exome

AF:

0.00747

GnomAD4 genome

AF:

0.00619

AC:

943

AN:

152270

Hom.:

Cov.:

AF XY:

0.00643

AC XY:

479

AN XY:

74452

show subpopulations

Gnomad4 AFR

AF:

0.00130

Gnomad4 AMR

AF:

0.00595

Gnomad4 ASJ

AF:

0.0141

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00103

Gnomad4 FIN

AF:

0.0167

Gnomad4 NFE

AF:

0.00779

Gnomad4 OTH

AF:

0.00710

Alfa

AF:

0.00719

Hom.:

Bravo

AF:

0.00517

Asia WGS

AF:

0.00231

AC:

AN:

3478

EpiCase

AF:

0.00791

EpiControl

AF:

0.00767

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Nov 14, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

CADD

Benign

1.4

DANN

Benign

0.85

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