rs13336428

Variant names:

• chr16-1482462-G-A
• rs13336428

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 0.531 in 152,016 control chromosomes in the GnomAD database, including 23,573 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 0.53 (23573 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257
• Publications: 50 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80558 AN: 151898 Hom.: 23533 Cov.: 32

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.478

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

GnomAD4 genome AF: 0.531 AC: 80645 AN: 152016 Hom.: 23573 Cov.: 32 AF XY: 0.532 AC XY: 39550 AN XY: 74288

African (AFR) AF: 0.777 AC: 32248 AN: 41480

American (AMR) AF: 0.449 AC: 6844 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1529 AN: 3468

East Asian (EAS) AF: 0.696 AC: 3588 AN: 5156

South Asian (SAS) AF: 0.594 AC: 2868 AN: 4826

European-Finnish (FIN) AF: 0.400 AC: 4233 AN: 10576

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.408 AC: 27708 AN: 67944

Other (OTH) AF: 0.474 AC: 1002 AN: 2114

Alfa AF: 0.448 Hom.: 71079

Bravo AF: 0.539

Asia WGS AF: 0.640 AC: 2223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.5
DANN	Benign	0.89
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs13336428; hg19: chr16-1532463;