rs282708

Variant names:

• chr4-58637561-A-G
• rs282708

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 0.528 in 152,046 control chromosomes in the GnomAD database, including 21,430 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 0.53 (21430 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.558 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: 0.528 AC: 80219 AN: 151928 Hom.: 21424 Cov.: 33

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.528 AC: 80249 AN: 152046 Hom.: 21430 Cov.: 33 AF XY: 0.522 AC XY: 38783 AN XY: 74342

African (AFR) AF: 0.511 AC: 21209 AN: 41484

American (AMR) AF: 0.512 AC: 7817 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1892 AN: 3468

East Asian (EAS) AF: 0.256 AC: 1322 AN: 5168

South Asian (SAS) AF: 0.423 AC: 2042 AN: 4826

European-Finnish (FIN) AF: 0.576 AC: 6100 AN: 10588

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.563 AC: 38238 AN: 67926

Other (OTH) AF: 0.525 AC: 1108 AN: 2110

Alfa AF: 0.550 Hom.: 71809

Bravo AF: 0.522

Asia WGS AF: 0.348 AC: 1207 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.8
DANN	Benign	0.79
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs282708; hg19: chr4-59503726;