22-20899293-C-T

Variant names:

• chr22-20899293-C-T
• rs178084

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 0.496 in 151,912 control chromosomes in the GnomAD database, including 19,250 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 0.50 (19250 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.585 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: 0.496 AC: 75335 AN: 151794 Hom.: 19230 Cov.: 32

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.496 AC: 75411 AN: 151912 Hom.: 19250 Cov.: 32 AF XY: 0.490 AC XY: 36385 AN XY: 74260

African (AFR) AF: 0.591 AC: 24506 AN: 41446

American (AMR) AF: 0.550 AC: 8378 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1676 AN: 3468

East Asian (EAS) AF: 0.581 AC: 2990 AN: 5142

South Asian (SAS) AF: 0.407 AC: 1962 AN: 4816

European-Finnish (FIN) AF: 0.293 AC: 3093 AN: 10562

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.457 AC: 31016 AN: 67930

Other (OTH) AF: 0.522 AC: 1097 AN: 2102

Alfa AF: 0.459 Hom.: 8828

Bravo AF: 0.522

Asia WGS AF: 0.490 AC: 1702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.26
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs178084; hg19: chr22-21253581;