Genetic Variant LRRC43:c.-406+3023T>G (chr12-122170805-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_152759.5(LRRC43):c.-406+3023T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.68 in 151,436 control chromosomes in the GnomAD database, including 35,156 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 0.68 ( 35156 hom., cov: 27)

Consequence

LRRC43
NM_152759.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00700

Publications

18 publications found

Variant links:

Genes affected

LRRC43 (HGNC:28562): (leucine rich repeat containing 43)

LRRC43 links:

Genome browser will be placed here

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=-1.01).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRC43	NM_152759.5 link	c.-406+3023T>G		intron_variant	Intron 1 of 11		NP_689972.3	Q8N309-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRC43	ENST00000537729.5 link	c.-406+3023T>G		intron_variant	Intron 1 of 5	5		ENSP00000438751.1		F5H0N3

Frequencies

GnomAD3 genomes

AF:

0.680

AC:

102897

AN:

151316

Hom.:

35144

Cov.:

show subpopulations

Gnomad AFR

AF:

0.702

Gnomad AMI

AF:

0.583

Gnomad AMR

AF:

0.694

Gnomad ASJ

AF:

0.704

Gnomad EAS

AF:

0.779

Gnomad SAS

AF:

0.727

Gnomad FIN

AF:

0.600

Gnomad MID

AF:

0.766

Gnomad NFE

AF:

0.665

Gnomad OTH

AF:

0.682

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.680

AC:

102960

AN:

151436

Hom.:

35156

Cov.:

AF XY:

0.681

AC XY:

50337

AN XY:

73946

show subpopulations

African (AFR)

AF:

0.701

AC:

28942

AN:

41270

American (AMR)

AF:

0.694

AC:

10556

AN:

15218

Ashkenazi Jewish (ASJ)

AF:

0.704

AC:

2437

AN:

3464

East Asian (EAS)

AF:

0.778

AC:

3982

AN:

5116

South Asian (SAS)

AF:

0.726

AC:

3454

AN:

4756

European-Finnish (FIN)

AF:

0.600

AC:

6299

AN:

10496

Middle Eastern (MID)

AF:

0.762

AC:

224

AN:

294

European-Non Finnish (NFE)

AF:

0.665

AC:

45103

AN:

67814

Other (OTH)

AF:

0.683

AC:

1434

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1628

3257

4885

6514

8142

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

808

1616

2424

3232

4040

<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:

0.614

Hom.:

3863

Bravo

AF:

0.687

Asia WGS

AF:

0.717

AC:

2497

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

3.5

(source)

DANN

Benign

0.53

PhyloP100

-0.0070

Splicing

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