chr4-89225498-G-A

Variant names:

• chr4-89225498-G-A
• rs9307064

Variant summary

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

The variant allele was found at a frequency of 0.719 in 151,984 control chromosomes in the GnomAD database, including 39,872 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 0.72 (39872 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.916 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

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109171 AN: 151866 Hom.: 39825 Cov.: 31

Gnomad AFR AF: 0.803

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.938

Gnomad SAS AF: 0.866

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.695

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

GnomAD4 genome AF: 0.719 AC: 109276 AN: 151984 Hom.: 39872 Cov.: 31 AF XY: 0.725 AC XY: 53891 AN XY: 74300

African (AFR) AF: 0.803 AC: 33259 AN: 41444

American (AMR) AF: 0.740 AC: 11286 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 2157 AN: 3472

East Asian (EAS) AF: 0.938 AC: 4859 AN: 5178

South Asian (SAS) AF: 0.866 AC: 4167 AN: 4814

European-Finnish (FIN) AF: 0.699 AC: 7388 AN: 10568

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.648 AC: 44020 AN: 67952

Other (OTH) AF: 0.698 AC: 1468 AN: 2104

Alfa AF: 0.670 Hom.: 107057

Bravo AF: 0.720

Asia WGS AF: 0.865 AC: 3006 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.13
DANN	Benign	0.32
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs9307064; hg19: chr4-90146649;