dbSNP rs11200928: LRIT2:p.Leu86Leu (chr10-84224967-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001017924.5(LRIT2):c.258C>T(p.Leu86Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 1,613,762 control chromosomes in the GnomAD database, including 41,905 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 ( 3127 hom., cov: 32)

Exomes 𝑓: 0.23 ( 38778 hom. )

Consequence

LRIT2
NM_001017924.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.108

Publications

15 publications found

Variant links:

Genes affected

LRIT2 (HGNC:23443): (leucine rich repeat, Ig-like and transmembrane domains 2) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

LRIT2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BP7

Synonymous conserved (PhyloP=-0.108 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRIT2	NM_001017924.5 link	c.258C>T	p.Leu86Leu	synonymous_variant	Exon 2 of 3	ENST00000372113.7	NP_001017924.1	A6NDA9-1
LRIT2	NM_001284223.1 link	c.258C>T	p.Leu86Leu	synonymous_variant	Exon 2 of 4		NP_001271152.1	A6NDA9-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRIT2	ENST00000372113.7 link	c.258C>T	p.Leu86Leu	synonymous_variant	Exon 2 of 3	1	NM_001017924.5	ENSP00000361185.3		A6NDA9-1
LRIT2	ENST00000538192.5 link	c.258C>T	p.Leu86Leu	synonymous_variant	Exon 2 of 4	1		ENSP00000438264.1		A6NDA9-2

Frequencies

GnomAD3 genomes

AF:

0.185

AC:

28100

AN:

151966

Hom.:

3113

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0839

Gnomad AMI

AF:

0.246

Gnomad AMR

AF:

0.268

Gnomad ASJ

AF:

0.208

Gnomad EAS

AF:

0.335

Gnomad SAS

AF:

0.204

Gnomad FIN

AF:

0.113

Gnomad MID

AF:

0.193

Gnomad NFE

AF:

0.223

Gnomad OTH

AF:

0.208

GnomAD2 exomes

AF:

0.217

AC:

54460

AN:

251454

AF XY:

0.217

show subpopulations

Gnomad AFR exome

AF:

0.0847

Gnomad AMR exome

AF:

0.270

Gnomad ASJ exome

AF:

0.216

Gnomad EAS exome

AF:

0.330

Gnomad FIN exome

AF:

0.118

Gnomad NFE exome

AF:

0.222

Gnomad OTH exome

AF:

0.218

GnomAD4 exome

AF:

0.226

AC:

330649

AN:

1461678

Hom.:

38778

Cov.:

AF XY:

0.226

AC XY:

164155

AN XY:

727160

show subpopulations

African (AFR)

AF:

0.0780

AC:

2610

AN:

33478

American (AMR)

AF:

0.268

AC:

12005

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.214

AC:

5583

AN:

26136

East Asian (EAS)

AF:

0.303

AC:

12042

AN:

39698

South Asian (SAS)

AF:

0.208

AC:

17942

AN:

86252

European-Finnish (FIN)

AF:

0.124

AC:

6608

AN:

53414

Middle Eastern (MID)

AF:

0.227

AC:

1309

AN:

5768

European-Non Finnish (NFE)

AF:

0.233

AC:

258817

AN:

1111822

Other (OTH)

AF:

0.227

AC:

13733

AN:

60386

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.468

Heterozygous variant carriers

15543

31085

46628

62170

77713

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8946

17892

26838

35784

44730

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.185

AC:

28144

AN:

152084

Hom.:

3127

Cov.:

AF XY:

0.183

AC XY:

13600

AN XY:

74328

show subpopulations

African (AFR)

AF:

0.0845

AC:

3505

AN:

41498

American (AMR)

AF:

0.268

AC:

4095

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.208

AC:

721

AN:

3470

East Asian (EAS)

AF:

0.334

AC:

1722

AN:

5150

South Asian (SAS)

AF:

0.205

AC:

984

AN:

4806

European-Finnish (FIN)

AF:

0.113

AC:

1197

AN:

10592

Middle Eastern (MID)

AF:

0.173

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.224

AC:

15192

AN:

67972

Other (OTH)

AF:

0.216

AC:

453

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1137

2274

3410

4547

5684

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

294

588

882

1176

1470

<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:

0.210

Hom.:

2934

Bravo

AF:

0.194

Asia WGS

AF:

0.273

AC:

946

AN:

3478

EpiCase

AF:

0.224

EpiControl

AF:

0.232

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

6.3

(source)

DANN

Benign

0.71

PhyloP100

-0.11

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over