chr9-84564349-A-G

Variant names:

• chr9-84564349-A-G
• rs1866439
• ENST00000650453.1:n.979-18848A>G

Variant summary

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

The ENST00000650453.1(ENSG00000285987):​n.979-18848A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 151,916 control chromosomes in the GnomAD database, including 15,390 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 0.40 (15390 hom., cov: 32)
• Consequence: ENSG00000285987 ENST00000650453.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.390
• Publications: 1 publications found

Genes affected

ENSG00000285987 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650453.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285987	ENST00000650453.1		n.979-18848A>G		intron	N/A
	ENSG00000285987	ENST00000728338.1		n.1045+6295A>G		intron	N/A
	ENSG00000285987	ENST00000728339.1		n.784-14422A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60827 AN: 151798 Hom.: 15335 Cov.: 32

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.401 AC: 60951 AN: 151916 Hom.: 15390 Cov.: 32 AF XY: 0.401 AC XY: 29787 AN XY: 74276

African (AFR) AF: 0.715 AC: 29598 AN: 41376

American (AMR) AF: 0.382 AC: 5830 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 946 AN: 3470

East Asian (EAS) AF: 0.411 AC: 2121 AN: 5158

South Asian (SAS) AF: 0.382 AC: 1840 AN: 4818

European-Finnish (FIN) AF: 0.264 AC: 2786 AN: 10560

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.246 AC: 16692 AN: 67962

Other (OTH) AF: 0.365 AC: 767 AN: 2100

Alfa AF: 0.298 Hom.: 22330

Bravo AF: 0.425

Asia WGS AF: 0.471 AC: 1634 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	9.5
DANN	Benign	0.33
PhyloP100		0.39

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1866439;

hg19: chr9-87179264;