Variant rs11015624 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_003525.2(LRRC37A6P):n.2667C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 1,324,402 control chromosomes in the GnomAD database, including 29,304 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 ( 2810 hom., cov: 32)

Exomes 𝑓: 0.20 ( 26494 hom. )

Consequence

LRRC37A6P
NR_003525.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.28

Variant links:

Genes affected

(HGNC:):

links:

LRRC37A6P (HGNC:33746): (leucine rich repeat containing 37 member A6, pseudogene)

LRRC37A6P links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRRC37A6P	NR_003525.2 linkuse as main transcript	n.2667C>T		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
	ENST00000284414.4 linkuse as main transcript	n.923C>T	non_coding_transcript_exon_variant	1/1
LRRC37A6P	ENST00000448648.2 linkuse as main transcript	n.2154C>T	non_coding_transcript_exon_variant	1/1
	ENST00000574842.1 linkuse as main transcript	n.256-418G>A	intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.186

AC:

28326

AN:

152000

Hom.:

2803

Cov.:

show subpopulations

Gnomad AFR

AF:

0.186

Gnomad AMI

AF:

0.136

Gnomad AMR

AF:

0.205

Gnomad ASJ

AF:

0.163

Gnomad EAS

AF:

0.0135

Gnomad SAS

AF:

0.0534

Gnomad FIN

AF:

0.195

Gnomad MID

AF:

0.133

Gnomad NFE

AF:

0.206

Gnomad OTH

AF:

0.170

GnomAD3 exomes

AF:

0.177

AC:

44476

AN:

250942

Hom.:

4606

AF XY:

0.169

AC XY:

22906

AN XY:

135684

show subpopulations

Gnomad AFR exome

AF:

0.193

Gnomad AMR exome

AF:

0.258

Gnomad ASJ exome

AF:

0.166

Gnomad EAS exome

AF:

0.0123

Gnomad SAS exome

AF:

0.0575

Gnomad FIN exome

AF:

0.208

Gnomad NFE exome

AF:

0.205

Gnomad OTH exome

AF:

0.180

GnomAD4 exome

AF:

0.203

AC:

237722

AN:

1172284

Hom.:

26494

Cov.:

AF XY:

0.196

AC XY:

117023

AN XY:

595890

show subpopulations

Gnomad4 AFR exome

AF:

0.197

Gnomad4 AMR exome

AF:

0.255

Gnomad4 ASJ exome

AF:

0.163

Gnomad4 EAS exome

AF:

0.0172

Gnomad4 SAS exome

AF:

0.0615

Gnomad4 FIN exome

AF:

0.212

Gnomad4 NFE exome

AF:

0.224

Gnomad4 OTH exome

AF:

0.187

GnomAD4 genome

AF:

0.186

AC:

28350

AN:

152118

Hom.:

2810

Cov.:

AF XY:

0.181

AC XY:

13459

AN XY:

74368

show subpopulations

Gnomad4 AFR

AF:

0.186

Gnomad4 AMR

AF:

0.206

Gnomad4 ASJ

AF:

0.163

Gnomad4 EAS

AF:

0.0135

Gnomad4 SAS

AF:

0.0530

Gnomad4 FIN

AF:

0.195

Gnomad4 NFE

AF:

0.206

Gnomad4 OTH

AF:

0.168

Alfa

AF:

0.199

Hom.:

579

Bravo

AF:

0.190

Asia WGS

AF:

0.0510

AC:

181

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.9

DANN

Benign

0.79

Splicing

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