9-120382296-A-G

Variant names:

• chr9-120382296-A-G
• rs10818453

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 0.681 in 150,788 control chromosomes in the GnomAD database, including 35,035 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 0.68 (35035 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.372

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.745 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: 0.681 AC: 102632 AN: 150672 Hom.: 35020 Cov.: 29

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.681 AC: 102691 AN: 150788 Hom.: 35035 Cov.: 29 AF XY: 0.684 AC XY: 50428 AN XY: 73682

Gnomad4 AFR AF: 0.633

Gnomad4 AMR AF: 0.732

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.765

Gnomad4 SAS AF: 0.664

Gnomad4 FIN AF: 0.772

Gnomad4 NFE AF: 0.682

Gnomad4 OTH AF: 0.678

Alfa AF: 0.690 Hom.: 12785

Bravo AF: 0.675

Asia WGS AF: 0.719 AC: 2502 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10818453; hg19: chr9-123144574;