rs4821554

chr22-36880042-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;