rs10857092

Variant names:

• chr4-122468064-G-A
• rs10857092

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 0.0922 in 152,064 control chromosomes in the GnomAD database, including 1,183 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 0.092 (1183 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.255

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 = 0.331 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: 0.0922 AC: 14009 AN: 151946 Hom.: 1181 Cov.: 32

Gnomad AFR AF: 0.0594

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.0187

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0591

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0675

Gnomad OTH AF: 0.0841

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

GnomAD4 genome AF: 0.0922 AC: 14021 AN: 152064 Hom.: 1183 Cov.: 32 AF XY: 0.0960 AC XY: 7133 AN XY: 74286

Gnomad4 AFR AF: 0.0593

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.0187

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.0591

Gnomad4 NFE AF: 0.0675

Gnomad4 OTH AF: 0.0851

Alfa AF: 0.0754 Hom.: 1473

Bravo AF: 0.108

Asia WGS AF: 0.189 AC: 655 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	2.3
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10857092; hg19: chr4-123389219;