4-54528857-A-T

Variant names:

• chr4-54528857-A-T
• rs218238

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 0.375 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.375 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

Gnomad4 AFR AF: 0.699

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.228

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.361

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs218238; hg19: chr4-55395024;