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. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.492 AC: 20320 AN: 41324

American (AMR) AF: 0.800 AC: 12209 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.782 AC: 2712 AN: 3466

East Asian (EAS) AF: 0.864 AC: 4387 AN: 5076

South Asian (SAS) AF: 0.674 AC: 3247 AN: 4820

European-Finnish (FIN) AF: 0.777 AC: 8183 AN: 10530

Middle Eastern (MID) AF: 0.647 AC: 189 AN: 292

European-Non Finnish (NFE) AF: 0.741 AC: 50219 AN: 67772

Other (OTH) AF: 0.713 AC: 1502 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.8
DANN	Benign	0.43
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs1424016; hg19: chr16-86543406;