rs4280783

Variant names:

• chr4-67223647-C-T
• rs4280783

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 0.428 in 152,020 control chromosomes in the GnomAD database, including 14,400 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 0.43 (14400 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 3 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 (AFR) allele frequency at 95% confidence interval = 0.541 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: 0.428 AC: 64978 AN: 151902 Hom.: 14373 Cov.: 33

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.428 AC: 65060 AN: 152020 Hom.: 14400 Cov.: 33 AF XY: 0.422 AC XY: 31396 AN XY: 74328

African (AFR) AF: 0.547 AC: 22709 AN: 41484

American (AMR) AF: 0.314 AC: 4794 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1492 AN: 3470

East Asian (EAS) AF: 0.369 AC: 1912 AN: 5176

South Asian (SAS) AF: 0.311 AC: 1499 AN: 4814

European-Finnish (FIN) AF: 0.385 AC: 4067 AN: 10558

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.399 AC: 27095 AN: 67934

Other (OTH) AF: 0.441 AC: 930 AN: 2110

Alfa AF: 0.407 Hom.: 8778

Bravo AF: 0.432

Asia WGS AF: 0.349 AC: 1209 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.13
DANN	Benign	0.22
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs4280783; hg19: chr4-68089365;