NM_203347.2:c.520+124G>A

Variant names:

• chr9-136762064-C-T
• rs2297721
• NM_203347.2:c.520+124G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_203347.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LCN15	NM_203347.2	MANE Select	c.520+124G>A		intron	N/A	NP_976222.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LCN15	ENST00000316144.6	TSL:1 MANE Select	c.520+124G>A		intron	N/A	ENSP00000313833.5
	LCN15	ENST00000482511.1	TSL:1	n.2670+124G>A		intron	N/A
	LCN15	ENST00000495223.1	TSL:5	n.208+1680G>A		intron	N/A

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

African (AFR) AF: 0.124 AC: 1791 AN: 14392

American (AMR) AF: 0.185 AC: 3140 AN: 16928

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 1925 AN: 14828

East Asian (EAS) AF: 0.129 AC: 3766 AN: 29294

South Asian (SAS) AF: 0.113 AC: 5240 AN: 46370

European-Finnish (FIN) AF: 0.105 AC: 4429 AN: 41984

Middle Eastern (MID) AF: 0.179 AC: 415 AN: 2322

European-Non Finnish (NFE) AF: 0.130 AC: 53788 AN: 413010

Other (OTH) AF: 0.141 AC: 4381 AN: 31034

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

African (AFR) AF: 0.125 AC: 5126 AN: 41048

American (AMR) AF: 0.184 AC: 2819 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 439 AN: 3468

East Asian (EAS) AF: 0.153 AC: 787 AN: 5148

South Asian (SAS) AF: 0.113 AC: 544 AN: 4818

European-Finnish (FIN) AF: 0.111 AC: 1178 AN: 10610

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9101 AN: 67916

Other (OTH) AF: 0.152 AC: 320 AN: 2108

Alfa AF: 0.134 Hom.: 765

Bravo AF: 0.142

Asia WGS AF: 0.148 AC: 516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.71
PhyloP100		-0.56
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2297721; hg19: chr9-139656516;