rs6722456

chr2-133771520-G-A

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 0.0454 in 152,302 control chromosomes in the GnomAD database, including 248 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 0.045 (248 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282

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 (EAS) allele frequency at 95% confidence interval = 0.147 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: 0.0454 AC: 6903 AN: 152184 Hom.: 248 Cov.: 33

Gnomad AFR AF: 0.0874

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0397

Gnomad ASJ AF: 0.0204

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.0234

Gnomad FIN AF: 0.00480

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0227

Gnomad OTH AF: 0.0334

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

GnomAD4 genome AF: 0.0454 AC: 6907 AN: 152302 Hom.: 248 Cov.: 33 AF XY: 0.0445 AC XY: 3313 AN XY: 74474

Gnomad4 AFR AF: 0.0873

Gnomad4 AMR AF: 0.0397

Gnomad4 ASJ AF: 0.0204

Gnomad4 EAS AF: 0.155

Gnomad4 SAS AF: 0.0238

Gnomad4 FIN AF: 0.00480

Gnomad4 NFE AF: 0.0227

Gnomad4 OTH AF: 0.0331

Alfa AF: 0.0409 Hom.: 24

Bravo AF: 0.0521

Asia WGS AF: 0.0810 AC: 280 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	3.0
Dann	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6722456; hg19: chr2-134529091;