chr22-16952320-T-G

Variant names:

• chr22-16952320-T-G
• rs4819923

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 0.393 in 152,044 control chromosomes in the GnomAD database, including 11,863 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 0.39 (11863 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59805 AN: 151926 Hom.: 11862 Cov.: 33

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.393 AC: 59824 AN: 152044 Hom.: 11863 Cov.: 33 AF XY: 0.393 AC XY: 29191 AN XY: 74306

African (AFR) AF: 0.371 AC: 15364 AN: 41452

American (AMR) AF: 0.406 AC: 6199 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1566 AN: 3466

East Asian (EAS) AF: 0.350 AC: 1808 AN: 5172

South Asian (SAS) AF: 0.530 AC: 2556 AN: 4820

European-Finnish (FIN) AF: 0.355 AC: 3751 AN: 10564

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27194 AN: 67968

Other (OTH) AF: 0.400 AC: 845 AN: 2112

Alfa AF: 0.406 Hom.: 9204

Bravo AF: 0.393

Asia WGS AF: 0.384 AC: 1337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.42
DANN	Benign	0.80
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4819923; hg19: chr22-17433210;