22-19743069-G-A

Variant names:

• chr22-19743069-G-A
• rs885988

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 0.605 in 152,036 control chromosomes in the GnomAD database, including 29,022 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 0.61 (29022 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.823
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.839 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: 0.605 AC: 91920 AN: 151918 Hom.: 28984 Cov.: 33

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.605 AC: 92016 AN: 152036 Hom.: 29022 Cov.: 33 AF XY: 0.608 AC XY: 45196 AN XY: 74326

African (AFR) AF: 0.751 AC: 31141 AN: 41458

American (AMR) AF: 0.648 AC: 9901 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1886 AN: 3470

East Asian (EAS) AF: 0.860 AC: 4437 AN: 5160

South Asian (SAS) AF: 0.624 AC: 3003 AN: 4816

European-Finnish (FIN) AF: 0.497 AC: 5255 AN: 10570

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.508 AC: 34525 AN: 67954

Other (OTH) AF: 0.592 AC: 1251 AN: 2112

Alfa AF: 0.540 Hom.: 40902

Bravo AF: 0.623

Asia WGS AF: 0.732 AC: 2544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.28
DANN	Benign	0.54
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs885988; hg19: chr22-19730592;