rs1886709

Variant names:

• chr9-25122216-A-G
• rs1886709
• ENST00000850879.1:n.212+20443A>G

Variant summary

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

The ENST00000850879.1(ENSG00000309091):​n.212+20443A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 151,916 control chromosomes in the GnomAD database, including 15,162 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 0.42 (15162 hom., cov: 32)
• Consequence: ENSG00000309091 ENST00000850879.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.249
• Publications: 4 publications found

Genes affected

ENSG00000309091 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309091	ENST00000850879.1	n.212+20443A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64562 AN: 151798 Hom.: 15175 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.410

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.425 AC: 64553 AN: 151916 Hom.: 15162 Cov.: 32 AF XY: 0.427 AC XY: 31664 AN XY: 74210

African (AFR) AF: 0.206 AC: 8535 AN: 41462

American (AMR) AF: 0.454 AC: 6936 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1458 AN: 3468

East Asian (EAS) AF: 0.673 AC: 3466 AN: 5150

South Asian (SAS) AF: 0.458 AC: 2206 AN: 4816

European-Finnish (FIN) AF: 0.540 AC: 5672 AN: 10502

Middle Eastern (MID) AF: 0.392 AC: 113 AN: 288

European-Non Finnish (NFE) AF: 0.511 AC: 34693 AN: 67948

Other (OTH) AF: 0.426 AC: 898 AN: 2108

Alfa AF: 0.482 Hom.: 73759

Bravo AF: 0.410

Asia WGS AF: 0.527 AC: 1830 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.87
DANN	Benign	0.54
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs1886709; hg19: chr9-25122214;