16-57355879-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 0.797 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.530

Gnomad4 AMR AF: 0.784

Gnomad4 ASJ AF: 0.933

Gnomad4 EAS AF: 0.810

Gnomad4 SAS AF: 0.737

Gnomad4 FIN AF: 0.946

Gnomad4 NFE AF: 0.934

Gnomad4 OTH AF: 0.835

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs223885; hg19: chr16-57389791;