4-3872325-C-T

Variant names:

• chr4-3872325-C-T
• rs28523451

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 0.289 in 151,820 control chromosomes in the GnomAD database, including 11,044 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 0.29 (11044 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43841 AN: 151702 Hom.: 11003 Cov.: 31

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.289 AC: 43942 AN: 151820 Hom.: 11044 Cov.: 31 AF XY: 0.293 AC XY: 21747 AN XY: 74168

African (AFR) AF: 0.678 AC: 28044 AN: 41352

American (AMR) AF: 0.188 AC: 2864 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 367 AN: 3470

East Asian (EAS) AF: 0.384 AC: 1953 AN: 5092

South Asian (SAS) AF: 0.257 AC: 1238 AN: 4808

European-Finnish (FIN) AF: 0.176 AC: 1860 AN: 10566

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6842 AN: 67952

Other (OTH) AF: 0.257 AC: 542 AN: 2110

Alfa AF: 0.168 Hom.: 10444

Bravo AF: 0.308

Asia WGS AF: 0.337 AC: 1172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.65
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs28523451; hg19: chr4-3874052;