rs4784379

Positions:

• chr16-54420064-A-G
• chr16-54420064-A-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 0.763 in 151,974 control chromosomes in the GnomAD database, including 44,276 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 0.76 (44276 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.977

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 (SAS) allele frequency at 95% confidence interval = 0.788 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: 0.763 AC: 115814 AN: 151856 Hom.: 44223 Cov.: 30

Gnomad AFR AF: 0.764

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.824

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.763 AC: 115922 AN: 151974 Hom.: 44276 Cov.: 30 AF XY: 0.766 AC XY: 56902 AN XY: 74284

Gnomad4 AFR AF: 0.764

Gnomad4 AMR AF: 0.707

Gnomad4 ASJ AF: 0.824

Gnomad4 EAS AF: 0.712

Gnomad4 SAS AF: 0.809

Gnomad4 FIN AF: 0.821

Gnomad4 NFE AF: 0.762

Gnomad4 OTH AF: 0.758

Alfa AF: 0.764 Hom.: 89893

Bravo AF: 0.755

Asia WGS AF: 0.725 AC: 2522 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	0.51
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4784379; hg19: chr16-54453976;