rs1022427

chr10-87846432-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0321 in 152,244 control chromosomes in the GnomAD database, including 112 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 0.032 (112 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0321 (4886/152244) while in subpopulation NFE AF= 0.0445 (3029/68016). AF 95% confidence interval is 0.0432. There are 112 homozygotes in gnomad4. There are 2384 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 112 gene

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: 0.0321 AC: 4887 AN: 152126 Hom.: 112 Cov.: 32

Gnomad AFR AF: 0.00872

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.0308

Gnomad ASJ AF: 0.0288

Gnomad EAS AF: 0.00673

Gnomad SAS AF: 0.0157

Gnomad FIN AF: 0.0625

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0445

Gnomad OTH AF: 0.0392

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

GnomAD4 genome AF: 0.0321 AC: 4886 AN: 152244 Hom.: 112 Cov.: 32 AF XY: 0.0320 AC XY: 2384 AN XY: 74432

Gnomad4 AFR AF: 0.00869

Gnomad4 AMR AF: 0.0308

Gnomad4 ASJ AF: 0.0288

Gnomad4 EAS AF: 0.00675

Gnomad4 SAS AF: 0.0155

Gnomad4 FIN AF: 0.0625

Gnomad4 NFE AF: 0.0445

Gnomad4 OTH AF: 0.0388

Alfa AF: 0.0407 Hom.: 26

Bravo AF: 0.0297

Asia WGS AF: 0.0110 AC: 39 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	0.68
Dann	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1022427; hg19: chr10-89606189;