4-3872325-C-T

Variant names:

• chr4-3872325-C-T
• rs28523451

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.289 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

Gnomad4 AFR AF: 0.678

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.257

Alfa AF: 0.142 Hom.: 2675

Bravo AF: 0.308

Asia WGS AF: 0.337 AC: 1172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28523451; hg19: chr4-3874052;