rs4821554

Variant names:

• chr22-36880042-A-G
• rs4821554

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 0.776 in 152,142 control chromosomes in the GnomAD database, including 46,071 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 0.78 (46071 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.838 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: 0.776 AC: 117965 AN: 152024 Hom.: 46020 Cov.: 32

Gnomad AFR AF: 0.845

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.719

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.694

Gnomad NFE AF: 0.742

Gnomad OTH AF: 0.767

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

GnomAD4 genome AF: 0.776 AC: 118071 AN: 152142 Hom.: 46071 Cov.: 32 AF XY: 0.778 AC XY: 57858 AN XY: 74376

African (AFR) AF: 0.845 AC: 35092 AN: 41524

American (AMR) AF: 0.804 AC: 12287 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.773 AC: 2685 AN: 3472

East Asian (EAS) AF: 0.670 AC: 3469 AN: 5176

South Asian (SAS) AF: 0.718 AC: 3464 AN: 4822

European-Finnish (FIN) AF: 0.782 AC: 8261 AN: 10566

Middle Eastern (MID) AF: 0.699 AC: 204 AN: 292

European-Non Finnish (NFE) AF: 0.742 AC: 50422 AN: 67984

Other (OTH) AF: 0.767 AC: 1619 AN: 2110

Alfa AF: 0.752 Hom.: 55954

Bravo AF: 0.780

Asia WGS AF: 0.748 AC: 2601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.61
DANN	Benign	0.31
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs4821554; hg19: chr22-37276084;