dbSNP rs1063162: LRRC42:c.-90T>C (chr1-53946508-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001256409.2(LRRC42):c.-90T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 151,872 control chromosomes in the GnomAD database, including 5,836 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 0.23 ( 5831 hom., cov: 31)

Exomes 𝑓: 0.15 ( 5 hom. )

Consequence

LRRC42
NM_001256409.2 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.103

Publications

6 publications found

Variant links:

Genes affected

LRRC42 (HGNC:28792): (leucine rich repeat containing 42)

LRRC42 links:

IFT25 (HGNC:25019): (intraflagellar transport 25) Predicted to enable metal ion binding activity. Predicted to be involved in kidney development and spermatogenesis. Predicted to act upstream of or within animal organ development; left/right axis specification; and skeletal system development. Predicted to be located in ciliary tip. Predicted to be part of intraciliary transport particle B. Predicted to be active in centrosome and cilium. [provided by Alliance of Genome Resources, Apr 2022]

IFT25 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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRC42	NM_001256409.2 link	c.-90T>C		5_prime_UTR_variant	Exon 1 of 9	ENST00000371370.8	NP_001243338.1	Q9Y546

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRC42	ENST00000371370.8 link	c.-90T>C		5_prime_UTR_variant	Exon 1 of 9	2	NM_001256409.2	ENSP00000360421.3		Q9Y546

Frequencies

GnomAD3 genomes

AF:

0.233

AC:

35289

AN:

151574

Hom.:

5804

Cov.:

show subpopulations

Gnomad AFR

AF:

0.471

Gnomad AMI

AF:

0.199

Gnomad AMR

AF:

0.134

Gnomad ASJ

AF:

0.181

Gnomad EAS

AF:

0.0600

Gnomad SAS

AF:

0.0761

Gnomad FIN

AF:

0.147

Gnomad MID

AF:

0.170

Gnomad NFE

AF:

0.152

Gnomad OTH

AF:

0.203

GnomAD4 exome

AF:

0.154

AC:

AN:

188

Hom.:

Cov.:

AF XY:

0.133

AC XY:

AN XY:

128

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.150

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.132

AC:

AN:

136

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.233

AC:

35362

AN:

151684

Hom.:

5831

Cov.:

AF XY:

0.228

AC XY:

16875

AN XY:

74140

show subpopulations

African (AFR)

AF:

0.472

AC:

19511

AN:

41360

American (AMR)

AF:

0.134

AC:

2048

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.181

AC:

628

AN:

3466

East Asian (EAS)

AF:

0.0600

AC:

307

AN:

5118

South Asian (SAS)

AF:

0.0762

AC:

367

AN:

4818

European-Finnish (FIN)

AF:

0.147

AC:

1546

AN:

10524

Middle Eastern (MID)

AF:

0.164

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.152

AC:

10298

AN:

67802

Other (OTH)

AF:

0.204

AC:

428

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1204

2408

3613

4817

6021

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

334

668

1002

1336

1670

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.198

Hom.:

500

Bravo

AF:

0.245

Asia WGS

AF:

0.106

AC:

357

AN:

3358

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

(source)

DANN

Benign

0.74

PhyloP100

-0.10

PromoterAI

0.0055

Neutral

(source)

Mutation Taster

=300/0

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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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