rs2297721

chr9-136762064-C-T

Variant summary

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

The NM_203347.2(LCN15):c.520+124G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 761,756 control chromosomes in the GnomAD database, including 6,893 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 0.14 (1458 hom., cov: 31)
  • Exomes 𝑓: 0.13 (5435 hom.)
• Consequence: LCN15 NM_203347.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.563

Genes affected

LCN15 (HGNC:33777): (lipocalin 15) Predicted to enable small molecule binding activity. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LCN15	NM_203347.2	c.520+124G>A		intron_variant		ENST00000316144.6
LCN15	XM_011518672.2	c.391+124G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LCN15	ENST00000316144.6	c.520+124G>A		intron_variant		1	NM_203347.2	P1
LCN15	ENST00000482511.1	n.2670+124G>A		intron_variant, non_coding_transcript_variant		1
LCN15	ENST00000495223.1	n.208+1680G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20492 AN: 151476 Hom.: 1452 Cov.: 31

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.153

GnomAD4 exome AF: 0.129 AC: 78875 AN: 610162 Hom.: 5435 AF XY: 0.129 AC XY: 40650 AN XY: 314390

Gnomad4 AFR exome AF: 0.124

Gnomad4 AMR exome AF: 0.185

Gnomad4 ASJ exome AF: 0.130

Gnomad4 EAS exome AF: 0.129

Gnomad4 SAS exome AF: 0.113

Gnomad4 FIN exome AF: 0.105

Gnomad4 NFE exome AF: 0.130

Gnomad4 OTH exome AF: 0.141

GnomAD4 genome AF: 0.135 AC: 20524 AN: 151594 Hom.: 1458 Cov.: 31 AF XY: 0.137 AC XY: 10159 AN XY: 74154

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.152

Alfa AF: 0.134 Hom.: 691

Bravo AF: 0.142

Asia WGS AF: 0.148 AC: 516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.6
Dann	Benign	0.71

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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

Other links and lift over

dbSNP: rs2297721; hg19: chr9-139656516;