16-56856988-G-T

Variant names:

• chr16-56856988-G-T
• rs1529930

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 0.879 in 152,124 control chromosomes in the GnomAD database, including 59,096 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 0.88 (59096 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.879 AC: 133611 AN: 152006 Hom.: 59039 Cov.: 30

Gnomad AFR AF: 0.961

Gnomad AMI AF: 0.889

Gnomad AMR AF: 0.913

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.933

Gnomad FIN AF: 0.801

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.876

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

GnomAD4 genome AF: 0.879 AC: 133727 AN: 152124 Hom.: 59096 Cov.: 30 AF XY: 0.882 AC XY: 65598 AN XY: 74380

African (AFR) AF: 0.961 AC: 39890 AN: 41514

American (AMR) AF: 0.913 AC: 13929 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.836 AC: 2902 AN: 3472

East Asian (EAS) AF: 0.995 AC: 5156 AN: 5182

South Asian (SAS) AF: 0.932 AC: 4488 AN: 4814

European-Finnish (FIN) AF: 0.801 AC: 8476 AN: 10578

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.823 AC: 55953 AN: 67992

Other (OTH) AF: 0.879 AC: 1854 AN: 2110

Alfa AF: 0.854 Hom.: 9402

Bravo AF: 0.892

Asia WGS AF: 0.958 AC: 3331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.51
PhyloP100		-0.019

Splicing

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

Other links and lift over

dbSNP: rs1529930; hg19: chr16-56890900;