rs1022427

Variant names:

• chr10-87846432-G-A
• rs1022427

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 112 gene

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: 0.0321 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

African (AFR) AF: 0.00869 AC: 361 AN: 41540

American (AMR) AF: 0.0308 AC: 470 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0288 AC: 100 AN: 3470

East Asian (EAS) AF: 0.00675 AC: 35 AN: 5188

South Asian (SAS) AF: 0.0155 AC: 75 AN: 4824

European-Finnish (FIN) AF: 0.0625 AC: 663 AN: 10606

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0445 AC: 3029 AN: 68016

Other (OTH) AF: 0.0388 AC: 82 AN: 2112

Alfa AF: 0.0419 Hom.: 33

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
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs1022427; hg19: chr10-89606189;