rs4819554

Variant names:

• chr22-17084145-G-A
• rs4819554

Your query was ambiguous. Multiple possible variants found:

• chr22-17084145-G-A
• chr22-17084145-G-C

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 0.831 in 152,194 control chromosomes in the GnomAD database, including 53,446 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 0.83 (53446 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.154
• Publications: 79 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.952 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: 0.831 AC: 126409 AN: 152076 Hom.: 53393 Cov.: 32

Gnomad AFR AF: 0.960

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.842

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.814

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

GnomAD4 genome AF: 0.831 AC: 126515 AN: 152194 Hom.: 53446 Cov.: 32 AF XY: 0.828 AC XY: 61596 AN XY: 74412

African (AFR) AF: 0.960 AC: 39896 AN: 41552

American (AMR) AF: 0.658 AC: 10046 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 2814 AN: 3472

East Asian (EAS) AF: 0.579 AC: 2987 AN: 5158

South Asian (SAS) AF: 0.762 AC: 3673 AN: 4820

European-Finnish (FIN) AF: 0.842 AC: 8928 AN: 10606

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.815 AC: 55392 AN: 68000

Other (OTH) AF: 0.813 AC: 1718 AN: 2112

Alfa AF: 0.806 Hom.: 71198

Bravo AF: 0.820

Asia WGS AF: 0.673 AC: 2338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.0
DANN	Benign	0.82
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs4819554; hg19: chr22-17565035;