rs4533449

Variant names:

• chr2-11365087-T-C
• rs4533449
• ENST00000430897.1:n.539+11A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-11365087-T-C
• chr2-11365087-T-G

Variant summary

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

The ENST00000430897.1(LINC03037):​n.539+11A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.697 in 152,230 control chromosomes in the GnomAD database, including 37,590 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 0.70 (37547 hom., cov: 31)
  • Exomes 𝑓: 0.84 (43 hom.)
• Consequence: LINC03037 ENST00000430897.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130
• Publications: 4 publications found

Genes affected

LINC03037 (HGNC:56227): (long intergenic non-protein coding RNA 3037)

PPIAP60 (HGNC:53684): (peptidylprolyl isomerase A pseudogene 60)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPIAP60	XM_047446546.1	c.502-59T>C		intron_variant	Intron 2 of 3		XP_047302502.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03037	ENST00000430897.1	n.539+11A>G		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.697 AC: 105968 AN: 151988 Hom.: 37495 Cov.: 31

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.662

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.832

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.736

Gnomad OTH AF: 0.653

GnomAD4 exome AF: 0.844 AC: 103 AN: 122 Hom.: 43 Cov.: 0 AF XY: 0.829 AC XY: 58 AN XY: 70

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.878 AC: 79 AN: 90

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.727 AC: 16 AN: 22

Other (OTH) AF: 1.00 AC: 4 AN: 4

GnomAD4 genome AF: 0.697 AC: 106073 AN: 152108 Hom.: 37547 Cov.: 31 AF XY: 0.700 AC XY: 52054 AN XY: 74340

African (AFR) AF: 0.605 AC: 25110 AN: 41488

American (AMR) AF: 0.745 AC: 11393 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2086 AN: 3470

East Asian (EAS) AF: 0.663 AC: 3415 AN: 5152

South Asian (SAS) AF: 0.606 AC: 2916 AN: 4814

European-Finnish (FIN) AF: 0.832 AC: 8820 AN: 10598

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.736 AC: 50033 AN: 67982

Other (OTH) AF: 0.650 AC: 1375 AN: 2114

Alfa AF: 0.714 Hom.: 119890

Bravo AF: 0.686

Asia WGS AF: 0.624 AC: 2172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.47
PhyloP100		-0.013
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Other links and lift over

dbSNP: rs4533449; hg19: chr2-11505213;