rs9307064

Positions:

• chr4-89225498-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.803

Gnomad4 AMR AF: 0.740

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.938

Gnomad4 SAS AF: 0.866

Gnomad4 FIN AF: 0.699

Gnomad4 NFE AF: 0.648

Gnomad4 OTH AF: 0.698

Alfa AF: 0.661 Hom.: 68511

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9307064; hg19: chr4-90146649;