12-25255530-A-G

Variant names:

• chr12-25255530-A-G
• rs12320328

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 0.107 in 152,264 control chromosomes in the GnomAD database, including 990 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 0.11 (990 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.157
• Publications: 16 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.148 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: 0.107 AC: 16224 AN: 152146 Hom.: 988 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.0615

Gnomad AMR AF: 0.0801

Gnomad ASJ AF: 0.0766

Gnomad EAS AF: 0.0454

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0845

Gnomad OTH AF: 0.0967

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

GnomAD4 genome AF: 0.107 AC: 16242 AN: 152264 Hom.: 990 Cov.: 32 AF XY: 0.109 AC XY: 8101 AN XY: 74462

African (AFR) AF: 0.151 AC: 6261 AN: 41548

American (AMR) AF: 0.0801 AC: 1226 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0766 AC: 266 AN: 3472

East Asian (EAS) AF: 0.0455 AC: 236 AN: 5190

South Asian (SAS) AF: 0.0998 AC: 482 AN: 4828

European-Finnish (FIN) AF: 0.165 AC: 1747 AN: 10596

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0845 AC: 5748 AN: 68014

Other (OTH) AF: 0.0956 AC: 202 AN: 2112

Alfa AF: 0.0867 Hom.: 1158

Bravo AF: 0.101

Asia WGS AF: 0.0880 AC: 305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.77
DANN	Benign	0.31
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs12320328; hg19: chr12-25408464;