rs7847869

Variant names:

• chr9-111973743-C-T
• rs7847869

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 0.134 in 152,184 control chromosomes in the GnomAD database, including 1,454 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 0.13 (1454 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.184 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: 0.134 AC: 20392 AN: 152066 Hom.: 1454 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.0512

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.134 AC: 20403 AN: 152184 Hom.: 1454 Cov.: 32 AF XY: 0.133 AC XY: 9912 AN XY: 74382

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.00270

Gnomad4 SAS AF: 0.0510

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.137

Alfa AF: 0.142 Hom.: 190

Bravo AF: 0.134

Asia WGS AF: 0.0380 AC: 133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
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: rs7847869; hg19: chr9-114736023;