rs7874083

Variant names:

• chr9-100720147-C-T
• rs7874083

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 0.216 in 152,068 control chromosomes in the GnomAD database, including 3,950 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 0.22 (3950 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.373 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: 0.216 AC: 32801 AN: 151950 Hom.: 3943 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.208

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.216 AC: 32841 AN: 152068 Hom.: 3950 Cov.: 32 AF XY: 0.220 AC XY: 16349 AN XY: 74316

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.237

Alfa AF: 0.194 Hom.: 1643

Bravo AF: 0.237

Asia WGS AF: 0.218 AC: 757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.8
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7874083; hg19: chr9-103482429;