rs2899383

Variant names:

• chr15-45804853-A-G
• rs2899383
• ENST00000559600.1:n.96-43728A>G

Variant summary

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

The ENST00000559600.1(ENSG00000259200):​n.96-43728A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 152,060 control chromosomes in the GnomAD database, including 28,982 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 0.61 (28982 hom., cov: 32)
• Consequence: ENSG00000259200 ENST00000559600.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.541
• Publications: 3 publications found

Genes affected

ENSG00000259200 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000559600.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105370802	NR_135680.1		n.96-43728A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259200	ENST00000559600.1	TSL:3	n.96-43728A>G		intron	N/A
	ENSG00000259200	ENST00000560705.1	TSL:3	n.556+12938A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93223 AN: 151942 Hom.: 28957 Cov.: 32

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.613 AC: 93288 AN: 152060 Hom.: 28982 Cov.: 32 AF XY: 0.616 AC XY: 45794 AN XY: 74334

African (AFR) AF: 0.581 AC: 24085 AN: 41444

American (AMR) AF: 0.517 AC: 7899 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2222 AN: 3466

East Asian (EAS) AF: 0.681 AC: 3531 AN: 5184

South Asian (SAS) AF: 0.630 AC: 3030 AN: 4810

European-Finnish (FIN) AF: 0.690 AC: 7314 AN: 10594

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.635 AC: 43186 AN: 67964

Other (OTH) AF: 0.624 AC: 1320 AN: 2114

Alfa AF: 0.610 Hom.: 4942

Bravo AF: 0.596

Asia WGS AF: 0.676 AC: 2350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.6
DANN	Benign	0.77
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs2899383; hg19: chr15-46097051;