rs9888325

chr12-109599608-G-T

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 0.485 in 152,062 control chromosomes in the GnomAD database, including 18,429 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 0.48 (18429 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.191

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73674 AN: 151944 Hom.: 18414 Cov.: 33

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.485 AC: 73739 AN: 152062 Hom.: 18429 Cov.: 33 AF XY: 0.477 AC XY: 35436 AN XY: 74334

Gnomad4 AFR AF: 0.479

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.207

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.457

Gnomad4 NFE AF: 0.533

Gnomad4 OTH AF: 0.518

Alfa AF: 0.527 Hom.: 2785

Bravo AF: 0.483

Asia WGS AF: 0.313 AC: 1089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.25
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9888325; hg19: chr12-110037413; COSMIC: COSV57332966;