rs7023148

chr9-10684803-C-Achr9-10684803-C-Gchr9-10684803-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;