5-28316550-G-T

Variant names:

• chr5-28316550-G-T
• rs2468449

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 0.264 in 151,972 control chromosomes in the GnomAD database, including 5,957 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 0.26 (5957 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.287
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.424 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: 0.264 AC: 40155 AN: 151852 Hom.: 5961 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.264 AC: 40160 AN: 151972 Hom.: 5957 Cov.: 32 AF XY: 0.265 AC XY: 19719 AN XY: 74282

African (AFR) AF: 0.127 AC: 5264 AN: 41482

American (AMR) AF: 0.264 AC: 4025 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1398 AN: 3472

East Asian (EAS) AF: 0.440 AC: 2262 AN: 5146

South Asian (SAS) AF: 0.365 AC: 1758 AN: 4820

European-Finnish (FIN) AF: 0.303 AC: 3205 AN: 10562

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21281 AN: 67944

Other (OTH) AF: 0.296 AC: 623 AN: 2106

Alfa AF: 0.302 Hom.: 4048

Bravo AF: 0.256

Asia WGS AF: 0.384 AC: 1335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.68
DANN	Benign	0.78
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs2468449; hg19: chr5-28316657;