rs2458179

Positions:

• chr17-46257341-G-A
• chr17-46257341-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047437205.1(LRRC37A):​c.101+9182G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 150,026 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.13 (0 hom., cov: 33)
• Consequence: LRRC37A XM_047437205.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.709

Genes affected

LRRC37A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRRC37A	XM_047437205.1	c.101+9182G>A		intron_variant			XP_047293161.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.125 AC: 18798 AN: 149916 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.0396

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.00156

Gnomad SAS AF: 0.0628

Gnomad FIN AF: 0.0608

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.163

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.125 AC: 18787 AN: 150026 Hom.: 0 Cov.: 33 AF XY: 0.118 AC XY: 8631 AN XY: 73354

Gnomad4 AFR AF: 0.0395

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.00156

Gnomad4 SAS AF: 0.0629

Gnomad4 FIN AF: 0.0608

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.162

Alfa AF: 0.0491 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.3
DANN	Benign	0.94

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2458179; hg19: chr17-44334707;