rs10857092

Variant names:

• chr4-122468064-G-A
• rs10857092

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 0.0922 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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0593 AC: 2460 AN: 41518

American (AMR) AF: 0.242 AC: 3686 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0187 AC: 65 AN: 3472

East Asian (EAS) AF: 0.345 AC: 1772 AN: 5142

South Asian (SAS) AF: 0.129 AC: 619 AN: 4810

European-Finnish (FIN) AF: 0.0591 AC: 625 AN: 10572

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0675 AC: 4591 AN: 67986

Other (OTH) AF: 0.0851 AC: 180 AN: 2114

Alfa AF: 0.0782 Hom.: 2556

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
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs10857092; hg19: chr4-123389219;