rs10428388

Variant names:

• chr4-56737516-C-T
• rs10428388

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 0.0873 in 152,120 control chromosomes in the GnomAD database, including 954 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 0.087 (954 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.341 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: 0.0873 AC: 13269 AN: 152002 Hom.: 949 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.0790

Gnomad ASJ AF: 0.0686

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.0194

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0475

Gnomad OTH AF: 0.0871

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

GnomAD4 genome AF: 0.0873 AC: 13282 AN: 152120 Hom.: 954 Cov.: 32 AF XY: 0.0908 AC XY: 6750 AN XY: 74368

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.0791

Gnomad4 ASJ AF: 0.0686

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.0194

Gnomad4 NFE AF: 0.0475

Gnomad4 OTH AF: 0.0862

Alfa AF: 0.0693 Hom.: 313

Bravo AF: 0.0930

Asia WGS AF: 0.243 AC: 845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.7
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10428388; hg19: chr4-57603682;