rs4820365

Variant names:

• chr22-39072910-G-A
• rs4820365

Your query was ambiguous. Multiple possible variants found:

• chr22-39072910-G-A
• chr22-39072910-G-T

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 0.268 in 151,676 control chromosomes in the GnomAD database, including 5,799 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 0.27 (5799 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.988
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40628 AN: 151558 Hom.: 5793 Cov.: 33

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.268 AC: 40656 AN: 151676 Hom.: 5799 Cov.: 33 AF XY: 0.273 AC XY: 20242 AN XY: 74142

African (AFR) AF: 0.190 AC: 7791 AN: 41102

American (AMR) AF: 0.241 AC: 3680 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1067 AN: 3472

East Asian (EAS) AF: 0.219 AC: 1132 AN: 5178

South Asian (SAS) AF: 0.314 AC: 1514 AN: 4820

European-Finnish (FIN) AF: 0.431 AC: 4544 AN: 10540

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19953 AN: 67978

Other (OTH) AF: 0.251 AC: 529 AN: 2110

Alfa AF: 0.171 Hom.: 380

Bravo AF: 0.248

Asia WGS AF: 0.235 AC: 817 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.6
DANN	Benign	0.83
PhyloP100		0.99
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs4820365; hg19: chr22-39468915;