rs4280783

chr4-67223647-C-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 0.428 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.547

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.430

Gnomad4 EAS AF: 0.369

Gnomad4 SAS AF: 0.311

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.399

Gnomad4 OTH AF: 0.441

Alfa AF: 0.402 Hom.: 5828

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4280783; hg19: chr4-68089365;