dbSNP rs3735171: LRRC61:c.-69A>G (chr7-150336793-A-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_001142928.2(LRRC61):c.-69A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 1,536,328 control chromosomes in the GnomAD database, including 52,867 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 0.27 ( 5790 hom., cov: 34)

Exomes 𝑓: 0.26 ( 47077 hom. )

Consequence

LRRC61
NM_001142928.2 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.21

Publications

18 publications found

Variant links:

Genes affected

LRRC61 (HGNC:21704): (leucine rich repeat containing 61) Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

LRRC61 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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
LRRC61	NM_001142928.2 link	c.-69A>G	5_prime_UTR_variant	Exon 3 of 3	ENST00000359623.9	NP_001136400.1	Q9BV99A0A090N7W5
LRRC61	NM_001363433.1 link	c.-69A>G	5_prime_UTR_variant	Exon 3 of 3		NP_001350362.1
LRRC61	NM_001363434.1 link	c.-69A>G	5_prime_UTR_variant	Exon 3 of 3		NP_001350363.1
LRRC61	NM_023942.3 link	c.-69A>G	5_prime_UTR_variant	Exon 2 of 2		NP_076431.1	Q9BV99A0A090N7W5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
LRRC61	ENST00000359623.9 link	c.-69A>G	5_prime_UTR_variant	Exon 3 of 3	2	NM_001142928.2	ENSP00000352642.4	Q9BV99
LRRC61	ENST00000323078.7 link	c.-69A>G	5_prime_UTR_variant	Exon 2 of 2	1		ENSP00000339047.6	Q9BV99
LRRC61	ENST00000493307.1 link	c.-69A>G	5_prime_UTR_variant	Exon 4 of 4	5		ENSP00000420560.1	Q9BV99

Frequencies

GnomAD3 genomes

AF:

0.271

AC:

41163

AN:

152144

Hom.:

5782

Cov.:

show subpopulations

Gnomad AFR

AF:

0.330

Gnomad AMI

AF:

0.390

Gnomad AMR

AF:

0.167

Gnomad ASJ

AF:

0.311

Gnomad EAS

AF:

0.292

Gnomad SAS

AF:

0.285

Gnomad FIN

AF:

0.250

Gnomad MID

AF:

0.263

Gnomad NFE

AF:

0.255

Gnomad OTH

AF:

0.246

GnomAD4 exome

AF:

0.258

AC:

357307

AN:

1384064

Hom.:

47077

Cov.:

AF XY:

0.259

AC XY:

176171

AN XY:

680058

show subpopulations

African (AFR)

AF:

0.339

AC:

10864

AN:

32080

American (AMR)

AF:

0.119

AC:

4545

AN:

38286

Ashkenazi Jewish (ASJ)

AF:

0.323

AC:

6973

AN:

21580

East Asian (EAS)

AF:

0.346

AC:

13524

AN:

39050

South Asian (SAS)

AF:

0.282

AC:

21235

AN:

75356

European-Finnish (FIN)

AF:

0.257

AC:

10653

AN:

41382

Middle Eastern (MID)

AF:

0.246

AC:

1323

AN:

5370

European-Non Finnish (NFE)

AF:

0.255

AC:

273413

AN:

1073708

Other (OTH)

AF:

0.258

AC:

14777

AN:

57252

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

15152

30304

45457

60609

75761

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9518

19036

28554

38072

47590

<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:

0.271

AC:

41207

AN:

152264

Hom.:

5790

Cov.:

AF XY:

0.270

AC XY:

20081

AN XY:

74450

show subpopulations

African (AFR)

AF:

0.331

AC:

13757

AN:

41552

American (AMR)

AF:

0.167

AC:

2557

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.311

AC:

1079

AN:

3470

East Asian (EAS)

AF:

0.291

AC:

1508

AN:

5182

South Asian (SAS)

AF:

0.285

AC:

1373

AN:

4824

European-Finnish (FIN)

AF:

0.250

AC:

2650

AN:

10610

Middle Eastern (MID)

AF:

0.245

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.255

AC:

17342

AN:

68004

Other (OTH)

AF:

0.243

AC:

514

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1607

3213

4820

6426

8033

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

432

864

1296

1728

2160

<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:

0.248

Hom.:

1233

Bravo

AF:

0.264

Asia WGS

AF:

0.290

AC:

1013

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.020

(source)

DANN

Benign

0.38

PhyloP100

-2.2

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over