rs4821467

Variant names:

• chr22-36220154-G-A
• rs4821467

Your query was ambiguous. Multiple possible variants found:

• chr22-36220154-G-A
• chr22-36220154-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 0.15 in 152,166 control chromosomes in the GnomAD database, including 2,942 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 0.15 (2942 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.349 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: 0.150 AC: 22864 AN: 152048 Hom.: 2939 Cov.: 32

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.0772

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.0593

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.0369

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0717

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.150 AC: 22875 AN: 152166 Hom.: 2942 Cov.: 32 AF XY: 0.147 AC XY: 10958 AN XY: 74418

African (AFR) AF: 0.354 AC: 14669 AN: 41466

American (AMR) AF: 0.0771 AC: 1180 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 366 AN: 3470

East Asian (EAS) AF: 0.0591 AC: 306 AN: 5182

South Asian (SAS) AF: 0.152 AC: 733 AN: 4820

European-Finnish (FIN) AF: 0.0369 AC: 392 AN: 10616

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0717 AC: 4875 AN: 67994

Other (OTH) AF: 0.123 AC: 260 AN: 2114

Alfa AF: 0.0785 Hom.: 397

Bravo AF: 0.161

Asia WGS AF: 0.118 AC: 413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.7
DANN	Benign	0.17
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs4821467; hg19: chr22-36616200;