Variant 7-150328826-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001142928.2(LRRC61):c.-145+2816G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,122 control chromosomes in the GnomAD database, including 4,492 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 0.24 ( 4489 hom., cov: 32)

Exomes 𝑓: 0.23 ( 3 hom. )

Consequence

LRRC61
NM_001142928.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.366

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:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
LRRC61	NM_001142928.2 linkuse as main transcript	c.-145+2816G>T	intron_variant	ENST00000359623.9
LRRC61	NM_001363433.1 linkuse as main transcript	c.-145+2816G>T	intron_variant
LRRC61	NM_001363434.1 linkuse as main transcript	c.-145+2816G>T	intron_variant
LRRC61	NM_023942.3 linkuse as main transcript	c.-145+5266G>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRC61	ENST00000359623.9 linkuse as main transcript	c.-145+2816G>T		intron_variant		2	NM_001142928.2	P1
	ENST00000343855.6 linkuse as main transcript	n.936G>T		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes

AF:

0.240

AC:

36455

AN:

151946

Hom.:

4490

Cov.:

show subpopulations

Gnomad AFR

AF:

0.232

Gnomad AMI

AF:

0.388

Gnomad AMR

AF:

0.156

Gnomad ASJ

AF:

0.310

Gnomad EAS

AF:

0.292

Gnomad SAS

AF:

0.271

Gnomad FIN

AF:

0.247

Gnomad MID

AF:

0.256

Gnomad NFE

AF:

0.251

Gnomad OTH

AF:

0.219

GnomAD4 exome

AF:

0.232

AC:

AN:

Hom.:

Cov.:

AF XY:

0.158

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.500

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.167

Gnomad4 NFE exome

AF:

0.250

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.240

AC:

36487

AN:

152066

Hom.:

4489

Cov.:

AF XY:

0.239

AC XY:

17789

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.233

Gnomad4 AMR

AF:

0.156

Gnomad4 ASJ

AF:

0.310

Gnomad4 EAS

AF:

0.291

Gnomad4 SAS

AF:

0.271

Gnomad4 FIN

AF:

0.247

Gnomad4 NFE

AF:

0.251

Gnomad4 OTH

AF:

0.216

Alfa

AF:

0.232

Hom.:

4190

Bravo

AF:

0.231

Asia WGS

AF:

0.279

AC:

973

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

0.64

Dann

Benign

0.80

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over