Variant rs4795404 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001195545.2(LRRC3C):c.-175+1724A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.757 in 152,090 control chromosomes in the GnomAD database, including 43,691 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 0.76 ( 43683 hom., cov: 32)

Exomes 𝑓: 0.94 ( 8 hom. )

Consequence

LRRC3C
NM_001195545.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0950

Variant links:

Genes affected

LRRC3C (HGNC:40034): (leucine rich repeat containing 3C) Predicted to be integral component of membrane. Predicted to be active in extracellular matrix and extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

LRRC3C links:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRRC3C	NM_001195545.2 linkuse as main transcript	c.-175+1724A>C		intron_variant		ENST00000377924.6	NP_001182474.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LRRC3C	ENST00000377924.6 linkuse as main transcript	c.-175+1724A>C		intron_variant		3	NM_001195545.2	ENSP00000367157	P1
	ENST00000582263.1 linkuse as main transcript	n.161+305A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.757

AC:

114993

AN:

151954

Hom.:

43673

Cov.:

show subpopulations

Gnomad AFR

AF:

0.703

Gnomad AMI

AF:

0.670

Gnomad AMR

AF:

0.724

Gnomad ASJ

AF:

0.767

Gnomad EAS

AF:

0.736

Gnomad SAS

AF:

0.774

Gnomad FIN

AF:

0.758

Gnomad MID

AF:

0.813

Gnomad NFE

AF:

0.797

Gnomad OTH

AF:

0.763

GnomAD4 exome

AF:

0.944

AC:

AN:

Hom.:

AF XY:

1.00

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

1.00

Gnomad4 NFE exome

AF:

0.900

Gnomad4 OTH exome

AF:

1.00

GnomAD4 genome

AF:

0.756

AC:

115042

AN:

152072

Hom.:

43683

Cov.:

AF XY:

0.752

AC XY:

55907

AN XY:

74342

show subpopulations

Gnomad4 AFR

AF:

0.702

Gnomad4 AMR

AF:

0.723

Gnomad4 ASJ

AF:

0.767

Gnomad4 EAS

AF:

0.736

Gnomad4 SAS

AF:

0.774

Gnomad4 FIN

AF:

0.758

Gnomad4 NFE

AF:

0.797

Gnomad4 OTH

AF:

0.762

Alfa

AF:

0.779

Hom.:

9502

Bravo

AF:

0.754

Asia WGS

AF:

0.721

AC:

2510

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.87

DANN

Benign

0.58

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over