chr22-47197663-A-G

Variant names:

• chr22-47197663-A-G
• rs9626698

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 0.192 in 152,086 control chromosomes in the GnomAD database, including 7,723 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 0.19 (7723 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.877
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29113 AN: 151968 Hom.: 7687 Cov.: 33

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0970

Gnomad ASJ AF: 0.0378

Gnomad EAS AF: 0.0303

Gnomad SAS AF: 0.0363

Gnomad FIN AF: 0.00461

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0263

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.192 AC: 29203 AN: 152086 Hom.: 7723 Cov.: 33 AF XY: 0.185 AC XY: 13737 AN XY: 74360

African (AFR) AF: 0.604 AC: 25036 AN: 41438

American (AMR) AF: 0.0968 AC: 1480 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0378 AC: 131 AN: 3468

East Asian (EAS) AF: 0.0302 AC: 156 AN: 5164

South Asian (SAS) AF: 0.0364 AC: 175 AN: 4812

European-Finnish (FIN) AF: 0.00461 AC: 49 AN: 10620

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0263 AC: 1790 AN: 67972

Other (OTH) AF: 0.148 AC: 313 AN: 2112

Alfa AF: 0.0880 Hom.: 7409

Bravo AF: 0.217

Asia WGS AF: 0.0840 AC: 292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	10
DANN	Benign	0.83
PhyloP100		0.88

Splicing

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

Other links and lift over

dbSNP: rs9626698; hg19: chr22-47593413;