rs10222962

Variant names:

• chr4-32391033-A-G
• rs10222962

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 0.105 in 152,196 control chromosomes in the GnomAD database, including 988 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 0.10 (988 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.406

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 (AFR) allele frequency at 95% confidence interval = 0.169 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: 0.105 AC: 15943 AN: 152078 Hom.: 985 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.0932

Gnomad ASJ AF: 0.0767

Gnomad EAS AF: 0.0306

Gnomad SAS AF: 0.0671

Gnomad FIN AF: 0.0471

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0859

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.105 AC: 15957 AN: 152196 Hom.: 988 Cov.: 32 AF XY: 0.102 AC XY: 7613 AN XY: 74422

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.0929

Gnomad4 ASJ AF: 0.0767

Gnomad4 EAS AF: 0.0307

Gnomad4 SAS AF: 0.0676

Gnomad4 FIN AF: 0.0471

Gnomad4 NFE AF: 0.0859

Gnomad4 OTH AF: 0.106

Alfa AF: 0.0924 Hom.: 426

Bravo AF: 0.111

Asia WGS AF: 0.0620 AC: 218 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	3.6
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10222962; hg19: chr4-32392655;