rs891725

Variant names:

• chr9-114084921-C-T
• rs891725

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 0.141 in 152,168 control chromosomes in the GnomAD database, including 2,201 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 0.14 (2201 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.247

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 (EAS) allele frequency at 95% confidence interval = 0.403 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: 0.141 AC: 21437 AN: 152050 Hom.: 2202 Cov.: 33

Gnomad AFR AF: 0.0321

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.0964

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.141 AC: 21437 AN: 152168 Hom.: 2201 Cov.: 33 AF XY: 0.151 AC XY: 11226 AN XY: 74374

Gnomad4 AFR AF: 0.0321

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.0964

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.147

Alfa AF: 0.145 Hom.: 2720

Bravo AF: 0.137

Asia WGS AF: 0.342 AC: 1186 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	6.1
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs891725; hg19: chr9-116847201;