rs12325410

Positions:

• chr16-9581389-T-G

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 0.166 in 152,144 control chromosomes in the GnomAD database, including 2,456 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 0.17 (2456 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.589

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.9581389T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000283003	ENST00000634367.2	n.574+14799T>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25305 AN: 152026 Hom.: 2458 Cov.: 31

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.0887

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.166 AC: 25326 AN: 152144 Hom.: 2456 Cov.: 31 AF XY: 0.166 AC XY: 12331 AN XY: 74372

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.0887

Gnomad4 EAS AF: 0.502

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.154

Alfa AF: 0.156 Hom.: 4346

Bravo AF: 0.172

Asia WGS AF: 0.325 AC: 1130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.5
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12325410; hg19: chr16-9675246;