rs4821554

Variant names:

• chr22-36880042-A-G
• rs4821554

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 0.776 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.845

Gnomad4 AMR AF: 0.804

Gnomad4 ASJ AF: 0.773

Gnomad4 EAS AF: 0.670

Gnomad4 SAS AF: 0.718

Gnomad4 FIN AF: 0.782

Gnomad4 NFE AF: 0.742

Gnomad4 OTH AF: 0.767

Alfa AF: 0.746 Hom.: 41938

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4821554; hg19: chr22-37276084;