rs6722456

Variant names:

• chr2-133771520-G-A
• rs6722456

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;