rs10428388

chr4-56737516-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;