rs7873820

chr9-24883181-C-Achr9-24883181-C-G

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 0.334 in 151,766 control chromosomes in the GnomAD database, including 14,399 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 0.33 (14399 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.774 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: 0.333 AC: 50563 AN: 151646 Hom.: 14338 Cov.: 32

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.334 AC: 50699 AN: 151766 Hom.: 14399 Cov.: 32 AF XY: 0.326 AC XY: 24202 AN XY: 74146

Gnomad4 AFR AF: 0.781

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.284

Alfa AF: 0.176 Hom.: 6187

Bravo AF: 0.352

Asia WGS AF: 0.275 AC: 957 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.015
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7873820; hg19: chr9-24883179; COSMIC: COSV69453823;