rs28517654

Variant names:

• chr4-55127301-T-C
• rs28517654

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 0.228 in 151,528 control chromosomes in the GnomAD database, including 4,295 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 0.23 (4295 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.50
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.274 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: 0.229 AC: 34612 AN: 151414 Hom.: 4297 Cov.: 30

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.228 AC: 34605 AN: 151528 Hom.: 4295 Cov.: 30 AF XY: 0.227 AC XY: 16782 AN XY: 73992

African (AFR) AF: 0.144 AC: 5963 AN: 41272

American (AMR) AF: 0.208 AC: 3168 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1214 AN: 3466

East Asian (EAS) AF: 0.180 AC: 926 AN: 5154

South Asian (SAS) AF: 0.253 AC: 1213 AN: 4800

European-Finnish (FIN) AF: 0.232 AC: 2405 AN: 10370

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.277 AC: 18848 AN: 67940

Other (OTH) AF: 0.243 AC: 508 AN: 2094

Alfa AF: 0.263 Hom.: 1126

Bravo AF: 0.222

Asia WGS AF: 0.193 AC: 670 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.87
DANN	Benign	0.72
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs28517654; hg19: chr4-55993468;