chr9-133317691-G-A

Variant names:

• chr9-133317691-G-A
• rs11244079
• ENST00000372030.3:n.-103G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000372030.3(LCN1P2):​n.-103G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0579 in 708,598 control chromosomes in the GnomAD database, including 1,749 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 0.047 (322 hom., cov: 32)
  • Exomes 𝑓: 0.061 (1427 hom.)
• Consequence: LCN1P2 ENST00000372030.3 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.59
• Publications: 14 publications found

Genes affected

LCN1P2 (HGNC:23680): (lipocalin 1 pseudogene 2)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0637 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000372030.3. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LCN1P2	ENST00000372030.3	TSL:6	n.-103G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.0473 AC: 7206 AN: 152190 Hom.: 322 Cov.: 32

Gnomad AFR AF: 0.00723

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0261

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0629

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0652

Gnomad OTH AF: 0.0350

GnomAD4 exome AF: 0.0608 AC: 33831 AN: 556290 Hom.: 1427 AF XY: 0.0623 AC XY: 17987 AN XY: 288936

African (AFR) AF: 0.00868 AC: 113 AN: 13020

American (AMR) AF: 0.0235 AC: 470 AN: 20034

Ashkenazi Jewish (ASJ) AF: 0.0628 AC: 882 AN: 14044

East Asian (EAS) AF: 0.000435 AC: 12 AN: 27570

South Asian (SAS) AF: 0.0762 AC: 3727 AN: 48910

European-Finnish (FIN) AF: 0.132 AC: 5333 AN: 40484

Middle Eastern (MID) AF: 0.0632 AC: 132 AN: 2088

European-Non Finnish (NFE) AF: 0.0599 AC: 21637 AN: 361500

Other (OTH) AF: 0.0532 AC: 1525 AN: 28640

GnomAD4 genome AF: 0.0473 AC: 7209 AN: 152308 Hom.: 322 Cov.: 32 AF XY: 0.0500 AC XY: 3720 AN XY: 74462

African (AFR) AF: 0.00721 AC: 300 AN: 41590

American (AMR) AF: 0.0261 AC: 399 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0634 AC: 220 AN: 3472

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5174

South Asian (SAS) AF: 0.0636 AC: 307 AN: 4828

European-Finnish (FIN) AF: 0.133 AC: 1414 AN: 10604

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0653 AC: 4439 AN: 68022

Other (OTH) AF: 0.0341 AC: 72 AN: 2110

Alfa AF: 0.0582 Hom.: 220

Bravo AF: 0.0344

Asia WGS AF: 0.0260 AC: 89 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.6
DANN	Benign	0.69
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs11244079; hg19: chr9-136184526;