rs3124203

chr10-30510787-C-G

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 0.212 in 152,058 control chromosomes in the GnomAD database, including 3,945 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 0.21 (3945 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.102

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.269 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: 0.212 AC: 32206 AN: 151940 Hom.: 3946 Cov.: 32

Gnomad AFR AF: 0.0964

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.0786

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.212 AC: 32203 AN: 152058 Hom.: 3945 Cov.: 32 AF XY: 0.211 AC XY: 15676 AN XY: 74312

Gnomad4 AFR AF: 0.0961

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.0794

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.240

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.236

Alfa AF: 0.241 Hom.: 582

Bravo AF: 0.204

Asia WGS AF: 0.143 AC: 498 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	3.5
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3124203; hg19: chr10-30799716;