Variant 10-27250013-T-C 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.2294A>G 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 0.2 in 1,257,530 control chromosomes in the GnomAD database, including 31,731 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 0.21 ( 3993 hom., cov: 31)

Exomes 𝑓: 0.20 ( 27738 hom. )

Consequence

LRRC37A6P
NR_003525.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.297

Variant links:

Genes affected

LRRC37A6P (HGNC:):

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=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.457 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.2294A>G		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
LRRC37A6P	ENST00000284414.4 linkuse as main transcript	n.550A>G	non_coding_transcript_exon_variant	1/1	6
LRRC37A6P	ENST00000448648.2 linkuse as main transcript	n.1781A>G	non_coding_transcript_exon_variant	1/1	6
ENSG00000262412	ENST00000574842.1 linkuse as main transcript	n.256-45T>C	intron_variant		2

Frequencies

GnomAD3 genomes

AF:

0.212

AC:

32177

AN:

151834

Hom.:

3980

Cov.:

show subpopulations

Gnomad AFR

AF:

0.101

Gnomad AMI

AF:

0.248

Gnomad AMR

AF:

0.247

Gnomad ASJ

AF:

0.232

Gnomad EAS

AF:

0.471

Gnomad SAS

AF:

0.399

Gnomad FIN

AF:

0.243

Gnomad MID

AF:

0.263

Gnomad NFE

AF:

0.231

Gnomad OTH

AF:

0.236

GnomAD3 exomes

AF:

0.258

AC:

64540

AN:

250212

Hom.:

9308

AF XY:

0.266

AC XY:

36088

AN XY:

135608

show subpopulations

Gnomad AFR exome

AF:

0.102

Gnomad AMR exome

AF:

0.214

Gnomad ASJ exome

AF:

0.238

Gnomad EAS exome

AF:

0.467

Gnomad SAS exome

AF:

0.384

Gnomad FIN exome

AF:

0.237

Gnomad NFE exome

AF:

0.232

Gnomad OTH exome

AF:

0.250

GnomAD4 exome

AF:

0.199

AC:

219872

AN:

1105578

Hom.:

27738

Cov.:

AF XY:

0.209

AC XY:

117939

AN XY:

564834

show subpopulations

Gnomad4 AFR exome

AF:

0.0840

Gnomad4 AMR exome

AF:

0.214

Gnomad4 ASJ exome

AF:

0.225

Gnomad4 EAS exome

AF:

0.494

Gnomad4 SAS exome

AF:

0.359

Gnomad4 FIN exome

AF:

0.230

Gnomad4 NFE exome

AF:

0.168

Gnomad4 OTH exome

AF:

0.212

GnomAD4 genome

AF:

0.212

AC:

32202

AN:

151952

Hom.:

3993

Cov.:

AF XY:

0.218

AC XY:

16173

AN XY:

74258

show subpopulations

Gnomad4 AFR

AF:

0.101

Gnomad4 AMR

AF:

0.247

Gnomad4 ASJ

AF:

0.232

Gnomad4 EAS

AF:

0.472

Gnomad4 SAS

AF:

0.399

Gnomad4 FIN

AF:

0.243

Gnomad4 NFE

AF:

0.231

Gnomad4 OTH

AF:

0.244

Alfa

AF:

0.221

Hom.:

765

Bravo

AF:

0.204

Asia WGS

AF:

0.432

AC:

1500

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

1.6

DANN

Benign

0.38

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