chr22-39439582-A-G

Variant names:

• chr22-39439582-A-G
• rs4821897

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 0.751 in 152,142 control chromosomes in the GnomAD database, including 43,275 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 0.75 (43275 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270
• Publications: 21 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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: 0.751 AC: 114221 AN: 152024 Hom.: 43233 Cov.: 32

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.883

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.751 AC: 114318 AN: 152142 Hom.: 43275 Cov.: 32 AF XY: 0.755 AC XY: 56134 AN XY: 74384

African (AFR) AF: 0.747 AC: 30995 AN: 41482

American (AMR) AF: 0.797 AC: 12180 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.682 AC: 2366 AN: 3468

East Asian (EAS) AF: 0.998 AC: 5181 AN: 5192

South Asian (SAS) AF: 0.883 AC: 4258 AN: 4822

European-Finnish (FIN) AF: 0.727 AC: 7695 AN: 10582

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.725 AC: 49302 AN: 67998

Other (OTH) AF: 0.728 AC: 1537 AN: 2112

Alfa AF: 0.739 Hom.: 61969

Bravo AF: 0.756

Asia WGS AF: 0.932 AC: 3240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.46
PhyloP100		-0.027

Splicing

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

Other links and lift over

dbSNP: rs4821897; hg19: chr22-39835587;