rs12598047

Variant names:

• chr16-86019428-A-G
• rs12598047

Your query was ambiguous. Multiple possible variants found:

• chr16-86019428-A-G
• chr16-86019428-A-T

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 0.0862 in 152,304 control chromosomes in the GnomAD database, including 1,465 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 0.086 (1465 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.567 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: 0.0862 AC: 13116 AN: 152186 Hom.: 1465 Cov.: 33

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0483

Gnomad ASJ AF: 0.0665

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0222

Gnomad OTH AF: 0.0764

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

GnomAD4 genome AF: 0.0862 AC: 13135 AN: 152304 Hom.: 1465 Cov.: 33 AF XY: 0.0961 AC XY: 7160 AN XY: 74482

Gnomad4 AFR AF: 0.129

Gnomad4 AMR AF: 0.0488

Gnomad4 ASJ AF: 0.0665

Gnomad4 EAS AF: 0.584

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.0222

Gnomad4 OTH AF: 0.0761

Alfa AF: 0.0442 Hom.: 191

Bravo AF: 0.0857

Asia WGS AF: 0.342 AC: 1187 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12598047; hg19: chr16-86053034;