Genetic Variant LRRC58:c.*6211G>A (chr3-120324989-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001099678.2(LRRC58):c.*6211G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 152,010 control chromosomes in the GnomAD database, including 3,877 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 0.19 ( 3877 hom., cov: 32)

Failed GnomAD Quality Control

Consequence

LRRC58
NM_001099678.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.211

Publications

16 publications found

Variant links:

Genes affected

LRRC58 (HGNC:26968): (leucine rich repeat containing 58)

LRRC58 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRC58	NM_001099678.2 link	c.*6211G>A		3_prime_UTR_variant	Exon 4 of 4	ENST00000295628.4	NP_001093148.1	Q96CX6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRC58	ENST00000295628.4 link	c.*6211G>A		3_prime_UTR_variant	Exon 4 of 4	1	NM_001099678.2	ENSP00000295628.3		Q96CX6

Frequencies

GnomAD3 genomes

AF:

0.190

AC:

28865

AN:

151892

Hom.:

3843

Cov.:

show subpopulations

Gnomad AFR

AF:

0.361

Gnomad AMI

AF:

0.0866

Gnomad AMR

AF:

0.264

Gnomad ASJ

AF:

0.126

Gnomad EAS

AF:

0.105

Gnomad SAS

AF:

0.180

Gnomad FIN

AF:

0.0636

Gnomad MID

AF:

0.187

Gnomad NFE

AF:

0.102

Gnomad OTH

AF:

0.185

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AC:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.190

AC:

28953

AN:

152010

Hom.:

3877

Cov.:

AF XY:

0.191

AC XY:

14228

AN XY:

74314

show subpopulations

African (AFR)

AF:

0.361

AC:

14967

AN:

41410

American (AMR)

AF:

0.265

AC:

4038

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.126

AC:

436

AN:

3464

East Asian (EAS)

AF:

0.105

AC:

542

AN:

5184

South Asian (SAS)

AF:

0.178

AC:

860

AN:

4820

European-Finnish (FIN)

AF:

0.0636

AC:

673

AN:

10578

Middle Eastern (MID)

AF:

0.194

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.102

AC:

6914

AN:

67994

Other (OTH)

AF:

0.184

AC:

387

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1088

2176

3265

4353

5441

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.135

Hom.:

6087

Bravo

AF:

0.214

Asia WGS

AF:

0.162

AC:

563

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

3.6

(source)

DANN

Benign

0.35

PhyloP100

0.21

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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3-120324989-C-T

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over