rs4382428

Variant names:

• chr8-134882423-G-A
• rs4382428

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 0.428 in 151,988 control chromosomes in the GnomAD database, including 14,147 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 0.43 (14147 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.562 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: 0.428 AC: 65029 AN: 151870 Hom.: 14136 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.428 AC: 65085 AN: 151988 Hom.: 14147 Cov.: 32 AF XY: 0.430 AC XY: 31936 AN XY: 74286

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.527

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.579

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.426

Alfa AF: 0.422 Hom.: 1723

Bravo AF: 0.437

Asia WGS AF: 0.471 AC: 1637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.12
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4382428; hg19: chr8-135894666;