9-84564349-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724036	XR_001746805.1	n.600-18848A>G		intron_variant	Intron 4 of 13
LOC102724036	XR_007061622.1	n.3429+6295A>G		intron_variant	Intron 7 of 16
LOC102724036	XR_007061623.1	n.6209+6295A>G		intron_variant	Intron 7 of 20

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285987	ENST00000650453.1	n.979-18848A>G		intron_variant	Intron 3 of 6
ENSG00000285987	ENST00000728338.1	n.1045+6295A>G		intron_variant	Intron 5 of 6
ENSG00000285987	ENST00000728339.1	n.784-14422A>G		intron_variant	Intron 3 of 5

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 v4.3

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

Other links and lift over

dbSNP: rs1866439; hg19: chr9-87179264;