rs2184033

Variant names:

• chr10-58064134-C-T
• rs2184033

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 0.553 in 152,014 control chromosomes in the GnomAD database, including 28,193 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 0.55 (28193 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.728 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: 0.554 AC: 84133 AN: 151896 Hom.: 28205 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.786

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.734

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.553 AC: 84122 AN: 152014 Hom.: 28193 Cov.: 32 AF XY: 0.552 AC XY: 41026 AN XY: 74318

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.693

Gnomad4 ASJ AF: 0.645

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.699

Gnomad4 FIN AF: 0.641

Gnomad4 NFE AF: 0.734

Gnomad4 OTH AF: 0.591

Alfa AF: 0.703 Hom.: 74427

Bravo AF: 0.538

Asia WGS AF: 0.611 AC: 2121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.12
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2184033; hg19: chr10-59823894;