rs11722802

Variant names:

• chr4-28722232-G-A
• rs11722802

Your query was ambiguous. Multiple possible variants found:

• chr4-28722232-G-A
• chr4-28722232-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0693 AC: 2875 AN: 41474

American (AMR) AF: 0.362 AC: 5511 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1123 AN: 3468

East Asian (EAS) AF: 0.584 AC: 2998 AN: 5136

South Asian (SAS) AF: 0.351 AC: 1689 AN: 4810

European-Finnish (FIN) AF: 0.212 AC: 2243 AN: 10566

Middle Eastern (MID) AF: 0.336 AC: 98 AN: 292

European-Non Finnish (NFE) AF: 0.254 AC: 17266 AN: 67876

Other (OTH) AF: 0.273 AC: 575 AN: 2110

Alfa AF: 0.254 Hom.: 5623

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
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs11722802; hg19: chr4-28723854;