rs4783880

Variant names:

• chr16-55122738-A-T
• rs4783880

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 0.212 in 152,182 control chromosomes in the GnomAD database, including 4,114 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 0.21 (4114 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.894
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.445 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: 0.212 AC: 32175 AN: 152064 Hom.: 4100 Cov.: 33

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.212 AC: 32221 AN: 152182 Hom.: 4114 Cov.: 33 AF XY: 0.216 AC XY: 16061 AN XY: 74408

African (AFR) AF: 0.297 AC: 12345 AN: 41498

American (AMR) AF: 0.260 AC: 3979 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 822 AN: 3468

East Asian (EAS) AF: 0.358 AC: 1852 AN: 5178

South Asian (SAS) AF: 0.461 AC: 2219 AN: 4814

European-Finnish (FIN) AF: 0.121 AC: 1286 AN: 10604

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9091 AN: 68010

Other (OTH) AF: 0.206 AC: 435 AN: 2110

Alfa AF: 0.170 Hom.: 334

Bravo AF: 0.228

Asia WGS AF: 0.400 AC: 1388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.82
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs4783880; hg19: chr16-55156650;