16-57355879-A-G

Variant names:

• chr16-57355879-A-G
• rs223885

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 0.797 in 151,728 control chromosomes in the GnomAD database, including 50,585 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 0.80 (50585 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.10
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.928 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: 0.797 AC: 120852 AN: 151612 Hom.: 50562 Cov.: 28

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.806

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.933

Gnomad EAS AF: 0.810

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.946

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.934

Gnomad OTH AF: 0.834

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

GnomAD4 genome AF: 0.797 AC: 120924 AN: 151728 Hom.: 50585 Cov.: 28 AF XY: 0.795 AC XY: 58962 AN XY: 74130

African (AFR) AF: 0.530 AC: 21858 AN: 41276

American (AMR) AF: 0.784 AC: 11933 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.933 AC: 3234 AN: 3468

East Asian (EAS) AF: 0.810 AC: 4177 AN: 5156

South Asian (SAS) AF: 0.737 AC: 3534 AN: 4792

European-Finnish (FIN) AF: 0.946 AC: 10003 AN: 10572

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.934 AC: 63427 AN: 67922

Other (OTH) AF: 0.835 AC: 1760 AN: 2108

Alfa AF: 0.861 Hom.: 6832

Bravo AF: 0.777

Asia WGS AF: 0.739 AC: 2571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.37
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs223885; hg19: chr16-57389791;