9-10684803-C-A

Variant names:

• chr9-10684803-C-A
• rs7023148

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 0.871 in 152,114 control chromosomes in the GnomAD database, including 58,119 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 0.87 (58119 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.953 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: 0.871 AC: 132347 AN: 151996 Hom.: 58088 Cov.: 31

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.874

Gnomad AMR AF: 0.905

Gnomad ASJ AF: 0.824

Gnomad EAS AF: 0.976

Gnomad SAS AF: 0.860

Gnomad FIN AF: 0.949

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.912

Gnomad OTH AF: 0.884

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

GnomAD4 genome AF: 0.871 AC: 132434 AN: 152114 Hom.: 58119 Cov.: 31 AF XY: 0.875 AC XY: 65091 AN XY: 74370

Gnomad4 AFR AF: 0.762

Gnomad4 AMR AF: 0.905

Gnomad4 ASJ AF: 0.824

Gnomad4 EAS AF: 0.975

Gnomad4 SAS AF: 0.860

Gnomad4 FIN AF: 0.949

Gnomad4 NFE AF: 0.912

Gnomad4 OTH AF: 0.881

Alfa AF: 0.901 Hom.: 83525

Bravo AF: 0.866

Asia WGS AF: 0.870 AC: 3026 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.79
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7023148; hg19: chr9-10684803;