rs1424016

Variant names:

• chr16-86509800-A-C
• rs1424016

Your query was ambiguous. Multiple possible variants found:

• chr16-86509800-A-C
• chr16-86509800-A-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 0.684 in 151,540 control chromosomes in the GnomAD database, including 36,526 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 0.68 (36526 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.698

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.843 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: 0.684 AC: 103510 AN: 151432 Hom.: 36501 Cov.: 35

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.782

Gnomad EAS AF: 0.864

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.653

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.684 AC: 103579 AN: 151540 Hom.: 36526 Cov.: 35 AF XY: 0.688 AC XY: 50924 AN XY: 74024

Gnomad4 AFR AF: 0.492

Gnomad4 AMR AF: 0.800

Gnomad4 ASJ AF: 0.782

Gnomad4 EAS AF: 0.864

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.777

Gnomad4 NFE AF: 0.741

Gnomad4 OTH AF: 0.713

Alfa AF: 0.615 Hom.: 1876

Bravo AF: 0.683

Asia WGS AF: 0.752 AC: 2598 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.8
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1424016; hg19: chr16-86543406;