22-19749901-C-G

Variant names:

• chr22-19749901-C-G
• rs16984141

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 0.173 in 152,100 control chromosomes in the GnomAD database, including 3,918 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 0.17 (3918 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.65
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26193 AN: 151982 Hom.: 3885 Cov.: 33

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.0868

Gnomad ASJ AF: 0.0570

Gnomad EAS AF: 0.0100

Gnomad SAS AF: 0.0524

Gnomad FIN AF: 0.0894

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0898

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.173 AC: 26284 AN: 152100 Hom.: 3918 Cov.: 33 AF XY: 0.168 AC XY: 12488 AN XY: 74368

African (AFR) AF: 0.410 AC: 17001 AN: 41426

American (AMR) AF: 0.0867 AC: 1325 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0570 AC: 198 AN: 3472

East Asian (EAS) AF: 0.0101 AC: 52 AN: 5174

South Asian (SAS) AF: 0.0519 AC: 250 AN: 4820

European-Finnish (FIN) AF: 0.0894 AC: 949 AN: 10612

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0898 AC: 6103 AN: 67988

Other (OTH) AF: 0.140 AC: 295 AN: 2112

Alfa AF: 0.0443 Hom.: 37

Bravo AF: 0.184

Asia WGS AF: 0.0830 AC: 292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.0070
DANN	Benign	0.39
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs16984141; hg19: chr22-19737424;