4-54528857-A-T

Variant names:

• chr4-54528857-A-T
• rs218238

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 0.375 in 152,148 control chromosomes in the GnomAD database, including 14,031 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 0.38 (14031 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.375 AC: 57002 AN: 152030 Hom.: 13969 Cov.: 32

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.375 AC: 57124 AN: 152148 Hom.: 14031 Cov.: 32 AF XY: 0.375 AC XY: 27894 AN XY: 74364

African (AFR) AF: 0.699 AC: 28999 AN: 41502

American (AMR) AF: 0.344 AC: 5253 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 874 AN: 3472

East Asian (EAS) AF: 0.336 AC: 1736 AN: 5170

South Asian (SAS) AF: 0.358 AC: 1722 AN: 4814

European-Finnish (FIN) AF: 0.228 AC: 2415 AN: 10580

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 15055 AN: 68008

Other (OTH) AF: 0.361 AC: 761 AN: 2106

Alfa AF: 0.311 Hom.: 1207

Bravo AF: 0.398

Asia WGS AF: 0.388 AC: 1347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.7
DANN	Benign	0.61
PhyloP100		0.018

Splicing

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

Other links and lift over

dbSNP: rs218238; hg19: chr4-55395024;