rs7852323

chr9-21174644-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 0.209 in 152,120 control chromosomes in the GnomAD database, including 3,676 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 0.21 (3676 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0420

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.404 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: 0.209 AC: 31706 AN: 152002 Hom.: 3669 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.209 AC: 31758 AN: 152120 Hom.: 3676 Cov.: 32 AF XY: 0.210 AC XY: 15604 AN XY: 74358

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.207

Alfa AF: 0.198 Hom.: 495

Bravo AF: 0.217

Asia WGS AF: 0.252 AC: 875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.9
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: rs7852323; hg19: chr9-21174643;