rs7873820

Variant names:

• chr9-24883181-C-A
• rs7873820

Your query was ambiguous. Multiple possible variants found:

• chr9-24883181-C-A
• chr9-24883181-C-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.781 AC: 32360 AN: 41438

American (AMR) AF: 0.179 AC: 2726 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 631 AN: 3468

East Asian (EAS) AF: 0.198 AC: 1020 AN: 5152

South Asian (SAS) AF: 0.181 AC: 871 AN: 4824

European-Finnish (FIN) AF: 0.159 AC: 1680 AN: 10558

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10722 AN: 67822

Other (OTH) AF: 0.284 AC: 596 AN: 2102

Alfa AF: 0.212 Hom.: 15072

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
PhyloP100		-2.1

Splicing

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

Other links and lift over

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