16-56917364-A-G

Position:

• chr16-56917364-A-G

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 0.584 in 152,084 control chromosomes in the GnomAD database, including 26,503 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 0.58 (26503 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.584 AC: 88792 AN: 151966 Hom.: 26487 Cov.: 33

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.598

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

GnomAD4 genome AF: 0.584 AC: 88852 AN: 152084 Hom.: 26503 Cov.: 33 AF XY: 0.583 AC XY: 43364 AN XY: 74342

Gnomad4 AFR AF: 0.692

Gnomad4 AMR AF: 0.545

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.621

Gnomad4 NFE AF: 0.550

Gnomad4 OTH AF: 0.593

Alfa AF: 0.559 Hom.: 31567

Bravo AF: 0.581

Asia WGS AF: 0.455 AC: 1581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.94
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28168; hg19: chr16-56951276;