16-56637720-A-T

Variant names:

• chr16-56637720-A-T
• rs60900828

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 0.116 in 152,118 control chromosomes in the GnomAD database, including 1,133 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 0.12 (1133 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.345
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.136 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: 0.116 AC: 17690 AN: 152000 Hom.: 1130 Cov.: 33

Gnomad AFR AF: 0.0922

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0816

Gnomad EAS AF: 0.00926

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.116 AC: 17708 AN: 152118 Hom.: 1133 Cov.: 33 AF XY: 0.114 AC XY: 8472 AN XY: 74356

African (AFR) AF: 0.0922 AC: 3827 AN: 41486

American (AMR) AF: 0.106 AC: 1627 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0816 AC: 283 AN: 3470

East Asian (EAS) AF: 0.00928 AC: 48 AN: 5174

South Asian (SAS) AF: 0.126 AC: 606 AN: 4824

European-Finnish (FIN) AF: 0.143 AC: 1508 AN: 10568

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9426 AN: 67992

Other (OTH) AF: 0.113 AC: 240 AN: 2116

Alfa AF: 0.0714 Hom.: 101

Bravo AF: 0.109

Asia WGS AF: 0.0690 AC: 241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.68
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs60900828; hg19: chr16-56671632;