rs4782390

Variant names:

• chr16-88640860-T-A
• rs4782390

Your query was ambiguous. Multiple possible variants found:

• chr16-88640860-T-A
• chr16-88640860-T-C
• chr16-88640860-T-G

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 0.702 in 152,202 control chromosomes in the GnomAD database, including 38,224 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 0.70 (38224 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.84 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.702 AC: 106758 AN: 152084 Hom.: 38173 Cov.: 34

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.702 AC: 106861 AN: 152202 Hom.: 38224 Cov.: 34 AF XY: 0.707 AC XY: 52585 AN XY: 74402

African (AFR) AF: 0.847 AC: 35191 AN: 41548

American (AMR) AF: 0.670 AC: 10252 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 2496 AN: 3470

East Asian (EAS) AF: 0.745 AC: 3850 AN: 5166

South Asian (SAS) AF: 0.755 AC: 3645 AN: 4830

European-Finnish (FIN) AF: 0.667 AC: 7067 AN: 10596

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.620 AC: 42168 AN: 67980

Other (OTH) AF: 0.693 AC: 1464 AN: 2114

Alfa AF: 0.521 Hom.: 1356

Bravo AF: 0.706

Asia WGS AF: 0.764 AC: 2659 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.60
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4782390; hg19: chr16-88707268;