dbSNP rs10762360: LRRC20:c.*1604C>G (chr10-70299750-G-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_001278212.2(LRRC20):c.*1604C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 152,842 control chromosomes in the GnomAD database, including 37,733 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 0.70 ( 37505 hom., cov: 31)

Exomes 𝑓: 0.74 ( 228 hom. )

Consequence

LRRC20
NM_001278212.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.419

Publications

7 publications found

Variant links:

Genes affected

LRRC20 (HGNC:23421): (leucine rich repeat containing 20)

LRRC20 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=-0.84).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001278212.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
LRRC20	NM_001278212.2	MANE Select	c.*1604C>G	3_prime_UTR	Exon 5 of 5	NP_001265141.1
LRRC20	NR_103467.2		n.2004C>G	non_coding_transcript_exon	Exon 3 of 3
LRRC20	NR_103468.2		n.1986C>G	non_coding_transcript_exon	Exon 3 of 3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
LRRC20	ENST00000446961.4	TSL:2 MANE Select	c.*1604C>G	3_prime_UTR	Exon 5 of 5	ENSP00000413745.2
LRRC20	ENST00000355790.8	TSL:1	c.*1604C>G	3_prime_UTR	Exon 5 of 5	ENSP00000348043.4
LRRC20	ENST00000373224.5	TSL:2	c.*1604C>G	3_prime_UTR	Exon 5 of 5	ENSP00000362321.1

Frequencies

GnomAD3 genomes

AF:

0.699

AC:

106146

AN:

151924

Hom.:

37483

Cov.:

show subpopulations

Gnomad AFR

AF:

0.659

Gnomad AMI

AF:

0.789

Gnomad AMR

AF:

0.633

Gnomad ASJ

AF:

0.600

Gnomad EAS

AF:

0.476

Gnomad SAS

AF:

0.652

Gnomad FIN

AF:

0.790

Gnomad MID

AF:

0.595

Gnomad NFE

AF:

0.748

Gnomad OTH

AF:

0.674

GnomAD4 exome

AF:

0.745

AC:

596

AN:

800

Hom.:

228

Cov.:

AF XY:

0.741

AC XY:

461

AN XY:

622

show subpopulations

African (AFR)

AF:

0.722

AC:

AN:

American (AMR)

AF:

0.417

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.750

AC:

AN:

East Asian (EAS)

AF:

0.412

AC:

AN:

South Asian (SAS)

AF:

0.600

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.760

AC:

508

AN:

668

Other (OTH)

AF:

0.794

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.515

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<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:

0.699

AC:

106215

AN:

152042

Hom.:

37505

Cov.:

AF XY:

0.699

AC XY:

51954

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.659

AC:

27337

AN:

41476

American (AMR)

AF:

0.633

AC:

9675

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.600

AC:

2082

AN:

3470

East Asian (EAS)

AF:

0.476

AC:

2445

AN:

5138

South Asian (SAS)

AF:

0.653

AC:

3152

AN:

4824

European-Finnish (FIN)

AF:

0.790

AC:

8358

AN:

10578

Middle Eastern (MID)

AF:

0.582

AC:

171

AN:

294

European-Non Finnish (NFE)

AF:

0.748

AC:

50867

AN:

67972

Other (OTH)

AF:

0.670

AC:

1412

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1630

3260

4889

6519

8149

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

820

1640

2460

3280

4100

<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:

0.726

Hom.:

5049

Bravo

AF:

0.681

Asia WGS

AF:

0.535

AC:

1861

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

7.4

(source)

DANN

Benign

0.73

PhyloP100

0.42

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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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over