Genetic Variant LRIG3-DT:n.512+13871G>A (chr12-59069979-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000716008.1(LRIG3-DT):n.512+13871G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0894 in 151,144 control chromosomes in the GnomAD database, including 980 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 0.089 ( 980 hom., cov: 32)

Consequence

LRIG3-DT
ENST00000716008.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0570

Publications

0 publications found

Variant links:

Genes affected

LRIG3-DT (HGNC:55476): (LRIG3 divergent transcript)

LRIG3-DT 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRIG3-DT	NR_183518.1 link	n.264+13871G>A		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LRIG3-DT	ENST00000716008.1 link	n.512+13871G>A	intron_variant	Intron 3 of 5
LRIG3-DT	ENST00000716009.1 link	n.553+5904G>A	intron_variant	Intron 6 of 7
LRIG3-DT	ENST00000716010.1 link	n.326+13871G>A	intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.0893

AC:

13480

AN:

151026

Hom.:

974

Cov.:

show subpopulations

Gnomad AFR

AF:

0.200

Gnomad AMI

AF:

0.00879

Gnomad AMR

AF:

0.111

Gnomad ASJ

AF:

0.0453

Gnomad EAS

AF:

0.0340

Gnomad SAS

AF:

0.0263

Gnomad FIN

AF:

0.0365

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.0371

Gnomad OTH

AF:

0.0999

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

GnomAD4 genome

AF:

0.0894

AC:

13508

AN:

151144

Hom.:

980

Cov.:

AF XY:

0.0873

AC XY:

6436

AN XY:

73740

show subpopulations

African (AFR)

AF:

0.200

AC:

8230

AN:

41216

American (AMR)

AF:

0.112

AC:

1687

AN:

15100

Ashkenazi Jewish (ASJ)

AF:

0.0453

AC:

157

AN:

3468

East Asian (EAS)

AF:

0.0341

AC:

176

AN:

5164

South Asian (SAS)

AF:

0.0259

AC:

124

AN:

4792

European-Finnish (FIN)

AF:

0.0365

AC:

379

AN:

10386

Middle Eastern (MID)

AF:

0.0952

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0371

AC:

2512

AN:

67720

Other (OTH)

AF:

0.0989

AC:

207

AN:

2094

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

591

1182

1773

2364

2955

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

138

276

414

552

690

<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:

0.0449

Hom.:

231

Bravo

AF:

0.0994

Asia WGS

AF:

0.0460

AC:

160

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.0

(source)

DANN

Benign

0.37

PhyloP100

0.057

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