dbSNP rs11769348: LRRC61:c.-145+3654T>C (chr7-150329664-T-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_001142928.2(LRRC61):c.-145+3654T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,252 control chromosomes in the GnomAD database, including 3,828 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 0.22 ( 3827 hom., cov: 33)

Exomes 𝑓: 0.31 ( 1 hom. )

Consequence

LRRC61
NM_001142928.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.381

Publications

21 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:

ENSG00000293476 (HGNC:):

ENSG00000293476 links:

ZBED10P (HGNC:21720): (zinc finger BED-type containing 10, pseudogene)

ZBED10P 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=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001142928.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
LRRC61	NM_001142928.2	MANE Select	c.-145+3654T>C	intron	N/A	NP_001136400.1	Q9BV99
LRRC61	NM_001363433.1		c.-145+3654T>C	intron	N/A	NP_001350362.1	Q9BV99
LRRC61	NM_001363434.1		c.-145+3654T>C	intron	N/A	NP_001350363.1	Q9BV99

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
LRRC61	ENST00000359623.9	TSL:2 MANE Select	c.-145+3654T>C	intron	N/A	ENSP00000352642.4	Q9BV99
LRRC61	ENST00000323078.7	TSL:1	c.-145+6104T>C	intron	N/A	ENSP00000339047.6	Q9BV99
LRRC61	ENST00000493307.1	TSL:5	c.-145+3654T>C	intron	N/A	ENSP00000420560.1	Q9BV99

Frequencies

GnomAD3 genomes

AF:

0.217

AC:

32969

AN:

152108

Hom.:

3836

Cov.:

show subpopulations

Gnomad AFR

AF:

0.151

Gnomad AMI

AF:

0.389

Gnomad AMR

AF:

0.148

Gnomad ASJ

AF:

0.310

Gnomad EAS

AF:

0.291

Gnomad SAS

AF:

0.271

Gnomad FIN

AF:

0.247

Gnomad MID

AF:

0.248

Gnomad NFE

AF:

0.251

Gnomad OTH

AF:

0.201

GnomAD4 exome

AF:

0.308

AC:

AN:

Hom.:

AF XY:

0.333

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.333

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.567

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.217

AC:

32975

AN:

152226

Hom.:

3827

Cov.:

AF XY:

0.218

AC XY:

16192

AN XY:

74418

show subpopulations

African (AFR)

AF:

0.152

AC:

6298

AN:

41524

American (AMR)

AF:

0.148

AC:

2265

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.310

AC:

1076

AN:

3470

East Asian (EAS)

AF:

0.290

AC:

1504

AN:

5178

South Asian (SAS)

AF:

0.270

AC:

1305

AN:

4828

European-Finnish (FIN)

AF:

0.247

AC:

2615

AN:

10598

Middle Eastern (MID)

AF:

0.236

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.251

AC:

17069

AN:

68014

Other (OTH)

AF:

0.198

AC:

419

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1326

2652

3979

5305

6631

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

358

716

1074

1432

1790

<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:

0.230

Hom.:

1487

Bravo

AF:

0.204

Asia WGS

AF:

0.270

AC:

942

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

3.0

(source)

DANN

Benign

0.77

PhyloP100

0.38

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