rs11722802

chr4-28722232-G-Achr4-28722232-G-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 0.227 in 151,872 control chromosomes in the GnomAD database, including 5,048 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 0.23 (5048 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.566 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: 0.227 AC: 34488 AN: 151754 Hom.: 5032 Cov.: 31

Gnomad AFR AF: 0.0695

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.227 AC: 34510 AN: 151872 Hom.: 5048 Cov.: 31 AF XY: 0.231 AC XY: 17180 AN XY: 74226

Gnomad4 AFR AF: 0.0693

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.584

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.273

Alfa AF: 0.256 Hom.: 4852

Bravo AF: 0.232

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.20
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11722802; hg19: chr4-28723854;