16-56856988-G-T

Position:

• chr16-56856988-G-T

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 0.879 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.961

Gnomad4 AMR AF: 0.913

Gnomad4 ASJ AF: 0.836

Gnomad4 EAS AF: 0.995

Gnomad4 SAS AF: 0.932

Gnomad4 FIN AF: 0.801

Gnomad4 NFE AF: 0.823

Gnomad4 OTH AF: 0.879

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1529930; hg19: chr16-56890900;