rs10428388

Variant names:

• chr4-56737516-C-T
• rs10428388

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 0.0873 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.124 AC: 5160 AN: 41476

American (AMR) AF: 0.0791 AC: 1210 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0686 AC: 238 AN: 3468

East Asian (EAS) AF: 0.355 AC: 1827 AN: 5150

South Asian (SAS) AF: 0.240 AC: 1157 AN: 4814

European-Finnish (FIN) AF: 0.0194 AC: 206 AN: 10592

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0475 AC: 3232 AN: 68008

Other (OTH) AF: 0.0862 AC: 182 AN: 2112

Alfa AF: 0.0700 Hom.: 1368

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
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs10428388; hg19: chr4-57603682;