rs891725

Variant names:

• chr9-114084921-C-T
• rs891725

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 0.141 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
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0321 AC: 1332 AN: 41548

American (AMR) AF: 0.245 AC: 3739 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0964 AC: 334 AN: 3466

East Asian (EAS) AF: 0.418 AC: 2153 AN: 5152

South Asian (SAS) AF: 0.230 AC: 1109 AN: 4828

European-Finnish (FIN) AF: 0.261 AC: 2764 AN: 10576

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9533 AN: 67996

Other (OTH) AF: 0.147 AC: 309 AN: 2108

Alfa AF: 0.143 Hom.: 3665

Bravo AF: 0.137

Asia WGS AF: 0.342 AC: 1186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.1
DANN	Benign	0.53
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs891725; hg19: chr9-116847201;