rs2184033

chr10-58064134-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;