rs2134133

chr3-21409056-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 0.0562 in 152,174 control chromosomes in the GnomAD database, including 582 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 0.056 (582 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.165 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: 0.0562 AC: 8542 AN: 152056 Hom.: 584 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0235

Gnomad ASJ AF: 0.00288

Gnomad EAS AF: 0.000387

Gnomad SAS AF: 0.00353

Gnomad FIN AF: 0.0592

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00701

Gnomad OTH AF: 0.0359

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

GnomAD4 genome AF: 0.0562 AC: 8556 AN: 152174 Hom.: 582 Cov.: 32 AF XY: 0.0575 AC XY: 4279 AN XY: 74406

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.0235

Gnomad4 ASJ AF: 0.00288

Gnomad4 EAS AF: 0.000388

Gnomad4 SAS AF: 0.00332

Gnomad4 FIN AF: 0.0592

Gnomad4 NFE AF: 0.00701

Gnomad4 OTH AF: 0.0355

Alfa AF: 0.0379 Hom.: 41

Bravo AF: 0.0579

Asia WGS AF: 0.00866 AC: 30 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.9
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2134133; hg19: chr3-21450548;