rs12325385

Variant names:

• chr16-8408213-C-A
• rs12325385

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 0.118 in 150,590 control chromosomes in the GnomAD database, including 1,125 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 0.12 (1125 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.938
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.129 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: 0.118 AC: 17695 AN: 150478 Hom.: 1127 Cov.: 29

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.0166

Gnomad SAS AF: 0.0886

Gnomad FIN AF: 0.0970

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.118 AC: 17707 AN: 150590 Hom.: 1125 Cov.: 29 AF XY: 0.114 AC XY: 8396 AN XY: 73470

African (AFR) AF: 0.111 AC: 4544 AN: 40944

American (AMR) AF: 0.104 AC: 1565 AN: 15052

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 761 AN: 3464

East Asian (EAS) AF: 0.0166 AC: 85 AN: 5106

South Asian (SAS) AF: 0.0893 AC: 424 AN: 4748

European-Finnish (FIN) AF: 0.0970 AC: 996 AN: 10268

Middle Eastern (MID) AF: 0.216 AC: 63 AN: 292

European-Non Finnish (NFE) AF: 0.131 AC: 8877 AN: 67712

Other (OTH) AF: 0.132 AC: 276 AN: 2098

Alfa AF: 0.133 Hom.: 1858

Bravo AF: 0.118

Asia WGS AF: 0.0540 AC: 188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.28
DANN	Benign	0.31
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs12325385; hg19: chr16-8458215;