rs12325385

Positions:

• chr16-8408213-C-A

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 0.118 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.0166

Gnomad4 SAS AF: 0.0893

Gnomad4 FIN AF: 0.0970

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.132

Alfa AF: 0.135 Hom.: 1451

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12325385; hg19: chr16-8458215;