chr22-37673615-G-A

Variant names:

• chr22-37673615-G-A
• rs13057866

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 0.0417 in 150,876 control chromosomes in the GnomAD database, including 275 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 0.042 (275 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.827
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0416 AC: 6270 AN: 150764 Hom.: 275 Cov.: 31

Gnomad AFR AF: 0.0681

Gnomad AMI AF: 0.0639

Gnomad AMR AF: 0.0609

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.0516

Gnomad FIN AF: 0.0141

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0146

Gnomad OTH AF: 0.0373

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

GnomAD4 genome AF: 0.0417 AC: 6288 AN: 150876 Hom.: 275 Cov.: 31 AF XY: 0.0427 AC XY: 3140 AN XY: 73620

African (AFR) AF: 0.0684 AC: 2796 AN: 40906

American (AMR) AF: 0.0611 AC: 921 AN: 15066

Ashkenazi Jewish (ASJ) AF: 0.0190 AC: 66 AN: 3470

East Asian (EAS) AF: 0.198 AC: 982 AN: 4968

South Asian (SAS) AF: 0.0514 AC: 245 AN: 4766

European-Finnish (FIN) AF: 0.0141 AC: 148 AN: 10530

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0146 AC: 990 AN: 67882

Other (OTH) AF: 0.0379 AC: 79 AN: 2086

Alfa AF: 0.0294 Hom.: 231

Bravo AF: 0.0516

Asia WGS AF: 0.115 AC: 398 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	9.8
DANN	Benign	0.64
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs13057866; hg19: chr22-38069622;