12-109599608-G-T

Variant names:

• chr12-109599608-G-T
• rs9888325

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 0.485 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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.479 AC: 19869 AN: 41480

American (AMR) AF: 0.407 AC: 6218 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1887 AN: 3470

East Asian (EAS) AF: 0.207 AC: 1070 AN: 5166

South Asian (SAS) AF: 0.379 AC: 1830 AN: 4824

European-Finnish (FIN) AF: 0.457 AC: 4828 AN: 10566

Middle Eastern (MID) AF: 0.551 AC: 161 AN: 292

European-Non Finnish (NFE) AF: 0.533 AC: 36248 AN: 67954

Other (OTH) AF: 0.518 AC: 1094 AN: 2114

Alfa AF: 0.516 Hom.: 26285

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
PhyloP100		-0.19

Splicing

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

Other links and lift over

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