chr22-44630624-G-A

Variant names:

• chr22-44630624-G-A
• rs6007220

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 0.299 in 151,950 control chromosomes in the GnomAD database, including 12,743 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 0.30 (12743 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 7 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 (AFR) allele frequency at 95% confidence interval = 0.738 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: 0.298 AC: 45260 AN: 151832 Hom.: 12689 Cov.: 31

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.0877

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.299 AC: 45369 AN: 151950 Hom.: 12743 Cov.: 31 AF XY: 0.293 AC XY: 21794 AN XY: 74268

African (AFR) AF: 0.745 AC: 30794 AN: 41344

American (AMR) AF: 0.199 AC: 3045 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 792 AN: 3466

East Asian (EAS) AF: 0.194 AC: 1003 AN: 5174

South Asian (SAS) AF: 0.170 AC: 816 AN: 4810

European-Finnish (FIN) AF: 0.0877 AC: 929 AN: 10594

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7246 AN: 67962

Other (OTH) AF: 0.272 AC: 573 AN: 2108

Alfa AF: 0.160 Hom.: 4743

Bravo AF: 0.324

Asia WGS AF: 0.230 AC: 802 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	0.040
DANN	Benign	0.59
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs6007220; hg19: chr22-45026504;