rs4784379

Variant names:

• chr16-54420064-A-G
• rs4784379
• ENST00000720695.1:n.183-46776A>G

Your query was ambiguous. Multiple possible variants found:

• chr16-54420064-A-G
• chr16-54420064-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000720695.1(ENSG00000287885):​n.183-46776A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000287885 ENST00000720695.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.977
• Publications: 9 publications found

Genes affected

ENSG00000287885 (HGNC:58975):

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 (SAS) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000720695.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287885	ENST00000720695.1		n.183-46776A>G		intron	N/A

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

African (AFR) AF: 0.764 AC: 31624 AN: 41390

American (AMR) AF: 0.707 AC: 10783 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.824 AC: 2855 AN: 3464

East Asian (EAS) AF: 0.712 AC: 3682 AN: 5168

South Asian (SAS) AF: 0.809 AC: 3888 AN: 4804

European-Finnish (FIN) AF: 0.821 AC: 8693 AN: 10588

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.762 AC: 51787 AN: 67986

Other (OTH) AF: 0.758 AC: 1598 AN: 2108

Alfa AF: 0.764 Hom.: 194856

Bravo AF: 0.755

Asia WGS AF: 0.725 AC: 2522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.51
DANN	Benign	0.40
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs4784379; hg19: chr16-54453976;