16-56637720-A-T

Variant names:

• chr16-56637720-A-T
• rs60900828

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0922

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.0816

Gnomad4 EAS AF: 0.00928

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.113

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs60900828; hg19: chr16-56671632;