chr22-30629202-A-G

Variant names:

• chr22-30629202-A-G
• rs731991

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 0.446 in 151,966 control chromosomes in the GnomAD database, including 15,787 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 0.45 (15787 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0540
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.502 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: 0.446 AC: 67745 AN: 151848 Hom.: 15776 Cov.: 31

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.446 AC: 67773 AN: 151966 Hom.: 15787 Cov.: 31 AF XY: 0.448 AC XY: 33247 AN XY: 74278

African (AFR) AF: 0.333 AC: 13817 AN: 41438

American (AMR) AF: 0.482 AC: 7359 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1803 AN: 3466

East Asian (EAS) AF: 0.195 AC: 1005 AN: 5146

South Asian (SAS) AF: 0.337 AC: 1624 AN: 4826

European-Finnish (FIN) AF: 0.588 AC: 6216 AN: 10564

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.507 AC: 34418 AN: 67952

Other (OTH) AF: 0.451 AC: 952 AN: 2112

Alfa AF: 0.482 Hom.: 26683

Bravo AF: 0.433

Asia WGS AF: 0.302 AC: 1054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.4
DANN	Benign	0.87
PhyloP100		0.054

Splicing

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

Other links and lift over

dbSNP: rs731991; hg19: chr22-31025189;