Variant chr8-144519798-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_014665.4(LRRC14):c.73T>C(p.Leu25=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.989 in 1,613,306 control chromosomes in the GnomAD database, including 790,801 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.99 ( 74288 hom., cov: 36)

Exomes 𝑓: 0.99 ( 716513 hom. )

Consequence

LRRC14
NM_014665.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.222

Variant links:

Genes affected

LRRC14 (HGNC:20419): (leucine rich repeat containing 14) This gene encodes a leucine-rich repeat-containing protein. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Dec 2012]

LRRC14 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.73).

BP6

Variant 8-144519798-T-C is Benign according to our data. Variant chr8-144519798-T-C is described in ClinVar as [Benign]. Clinvar id is 403369.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.222 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRRC14	NM_014665.4 linkuse as main transcript	c.73T>C	p.Leu25=	synonymous_variant	2/4	ENST00000292524.6	NP_055480.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LRRC14	ENST00000292524.6 linkuse as main transcript	c.73T>C	p.Leu25=	synonymous_variant	2/4	1	NM_014665.4	ENSP00000292524	P1

Frequencies

GnomAD3 genomes

AF:

0.987

AC:

150218

AN:

152246

Hom.:

74231

Cov.:

show subpopulations

Gnomad AFR

AF:

0.997

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.951

Gnomad ASJ

AF:

1.00

Gnomad EAS

AF:

0.796

Gnomad SAS

AF:

0.996

Gnomad FIN

AF:

0.998

Gnomad MID

AF:

1.00

Gnomad NFE

AF:

1.00

Gnomad OTH

AF:

0.989

GnomAD3 exomes

AF:

0.970

AC:

242698

AN:

250128

Hom.:

118201

AF XY:

0.976

AC XY:

132336

AN XY:

135654

show subpopulations

Gnomad AFR exome

AF:

0.998

Gnomad AMR exome

AF:

0.902

Gnomad ASJ exome

AF:

1.00

Gnomad EAS exome

AF:

0.796

Gnomad SAS exome

AF:

0.998

Gnomad FIN exome

AF:

0.997

Gnomad NFE exome

AF:

1.00

Gnomad OTH exome

AF:

0.982

GnomAD4 exome

AF:

0.989

AC:

1445313

AN:

1460942

Hom.:

716513

Cov.:

AF XY:

0.990

AC XY:

719452

AN XY:

726770

show subpopulations

Gnomad4 AFR exome

AF:

0.998

Gnomad4 AMR exome

AF:

0.908

Gnomad4 ASJ exome

AF:

1.00

Gnomad4 EAS exome

AF:

0.744

Gnomad4 SAS exome

AF:

0.999

Gnomad4 FIN exome

AF:

0.996

Gnomad4 NFE exome

AF:

1.00

Gnomad4 OTH exome

AF:

0.989

GnomAD4 genome

AF:

0.987

AC:

150334

AN:

152364

Hom.:

74288

Cov.:

AF XY:

0.985

AC XY:

73385

AN XY:

74500

show subpopulations

Gnomad4 AFR

AF:

0.997

Gnomad4 AMR

AF:

0.951

Gnomad4 ASJ

AF:

1.00

Gnomad4 EAS

AF:

0.795

Gnomad4 SAS

AF:

0.997

Gnomad4 FIN

AF:

0.998

Gnomad4 NFE

AF:

1.00

Gnomad4 OTH

AF:

0.989

Alfa

AF:

0.997

Hom.:

37541

Bravo

AF:

0.982

Asia WGS

AF:

0.943

AC:

3280

AN:

3478

EpiCase

AF:

1.00

EpiControl

AF:

1.00

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: MAF -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

6.8

DANN

Benign

0.78

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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