16-56605793-A-T

Variant names:

• chr16-56605793-A-T
• rs1811322

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 0.802 in 152,100 control chromosomes in the GnomAD database, including 49,271 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 0.80 (49271 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.174
• Publications: 7 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 = 0.825 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: 0.802 AC: 121938 AN: 151982 Hom.: 49239 Cov.: 32

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.806

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

GnomAD4 genome AF: 0.802 AC: 122013 AN: 152100 Hom.: 49271 Cov.: 32 AF XY: 0.797 AC XY: 59251 AN XY: 74348

African (AFR) AF: 0.832 AC: 34503 AN: 41472

American (AMR) AF: 0.665 AC: 10156 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.836 AC: 2902 AN: 3470

East Asian (EAS) AF: 0.681 AC: 3527 AN: 5176

South Asian (SAS) AF: 0.822 AC: 3963 AN: 4820

European-Finnish (FIN) AF: 0.758 AC: 8024 AN: 10580

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.827 AC: 56203 AN: 67996

Other (OTH) AF: 0.805 AC: 1702 AN: 2114

Alfa AF: 0.811 Hom.: 6238

Bravo AF: 0.791

Asia WGS AF: 0.728 AC: 2532 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	0.73
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs1811322; hg19: chr16-56639705;