chr22-49310652-T-C

Variant names:

• chr22-49310652-T-C
• rs2858522

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 0.856 in 152,186 control chromosomes in the GnomAD database, including 56,092 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 0.86 (56092 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.707
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.925 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: 0.856 AC: 130223 AN: 152068 Hom.: 56047 Cov.: 31

Gnomad AFR AF: 0.933

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.938

Gnomad SAS AF: 0.852

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.861

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

GnomAD4 genome AF: 0.856 AC: 130325 AN: 152186 Hom.: 56092 Cov.: 31 AF XY: 0.857 AC XY: 63742 AN XY: 74388

African (AFR) AF: 0.933 AC: 38735 AN: 41524

American (AMR) AF: 0.790 AC: 12086 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.843 AC: 2926 AN: 3470

East Asian (EAS) AF: 0.939 AC: 4845 AN: 5162

South Asian (SAS) AF: 0.852 AC: 4105 AN: 4820

European-Finnish (FIN) AF: 0.812 AC: 8601 AN: 10592

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.826 AC: 56196 AN: 67998

Other (OTH) AF: 0.861 AC: 1822 AN: 2116

Alfa AF: 0.840 Hom.: 67394

Bravo AF: 0.860

Asia WGS AF: 0.906 AC: 3154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.0040
DANN	Benign	0.33
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs2858522; hg19: chr22-49706577;