16-13809456-G-A

Variant names:

• chr16-13809456-G-A
• rs1573638

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 0.135 in 152,094 control chromosomes in the GnomAD database, including 2,063 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 0.14 (2063 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82
• Publications: 4 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 = 0.273 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: 0.135 AC: 20505 AN: 151976 Hom.: 2057 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.0659

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0660

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.135 AC: 20547 AN: 152094 Hom.: 2063 Cov.: 32 AF XY: 0.136 AC XY: 10089 AN XY: 74356

African (AFR) AF: 0.277 AC: 11497 AN: 41480

American (AMR) AF: 0.118 AC: 1806 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 445 AN: 3464

East Asian (EAS) AF: 0.120 AC: 620 AN: 5164

South Asian (SAS) AF: 0.108 AC: 519 AN: 4816

European-Finnish (FIN) AF: 0.0659 AC: 697 AN: 10572

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0660 AC: 4488 AN: 67992

Other (OTH) AF: 0.130 AC: 275 AN: 2112

Alfa AF: 0.0881 Hom.: 3616

Bravo AF: 0.149

Asia WGS AF: 0.121 AC: 422 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	0.050
DANN	Benign	0.42
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1573638; hg19: chr16-13903313;