rs28374251

Variant names:

• chr8-5350467-G-A
• rs28374251

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 0.346 in 151,894 control chromosomes in the GnomAD database, including 10,529 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 0.35 (10529 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.536 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: 0.346 AC: 52511 AN: 151776 Hom.: 10510 Cov.: 31

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.346 AC: 52564 AN: 151894 Hom.: 10529 Cov.: 31 AF XY: 0.348 AC XY: 25850 AN XY: 74224

African (AFR) AF: 0.542 AC: 22435 AN: 41396

American (AMR) AF: 0.434 AC: 6612 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1002 AN: 3470

East Asian (EAS) AF: 0.417 AC: 2144 AN: 5144

South Asian (SAS) AF: 0.315 AC: 1514 AN: 4812

European-Finnish (FIN) AF: 0.212 AC: 2231 AN: 10542

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15680 AN: 67958

Other (OTH) AF: 0.349 AC: 737 AN: 2114

Alfa AF: 0.326 Hom.: 1406

Bravo AF: 0.371

Asia WGS AF: 0.374 AC: 1300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.7
DANN	Benign	0.82
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs28374251; hg19: chr8-5207989;