16-56917364-A-G

Variant names:

• chr16-56917364-A-G
• rs28168

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 0.584 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
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.692 AC: 28687 AN: 41458

American (AMR) AF: 0.545 AC: 8334 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1930 AN: 3472

East Asian (EAS) AF: 0.315 AC: 1631 AN: 5180

South Asian (SAS) AF: 0.485 AC: 2337 AN: 4820

European-Finnish (FIN) AF: 0.621 AC: 6564 AN: 10568

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.550 AC: 37417 AN: 67978

Other (OTH) AF: 0.593 AC: 1254 AN: 2114

Alfa AF: 0.562 Hom.: 40608

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
PhyloP100		0.0070

Splicing

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

Other links and lift over

dbSNP: rs28168; hg19: chr16-56951276;