rs17753394

Variant names:

• chr22-38282381-T-G
• rs17753394

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 0.136 in 151,738 control chromosomes in the GnomAD database, including 1,582 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 0.14 (1582 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.601
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.228 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: 0.136 AC: 20642 AN: 151618 Hom.: 1583 Cov.: 30

Gnomad AFR AF: 0.0836

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.163

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.136 AC: 20634 AN: 151738 Hom.: 1582 Cov.: 30 AF XY: 0.136 AC XY: 10057 AN XY: 74096

African (AFR) AF: 0.0835 AC: 3455 AN: 41394

American (AMR) AF: 0.115 AC: 1749 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 576 AN: 3462

East Asian (EAS) AF: 0.105 AC: 539 AN: 5156

South Asian (SAS) AF: 0.240 AC: 1150 AN: 4800

European-Finnish (FIN) AF: 0.132 AC: 1385 AN: 10492

Middle Eastern (MID) AF: 0.164 AC: 48 AN: 292

European-Non Finnish (NFE) AF: 0.166 AC: 11276 AN: 67956

Other (OTH) AF: 0.138 AC: 290 AN: 2104

Alfa AF: 0.154 Hom.: 7283

Bravo AF: 0.127

Asia WGS AF: 0.175 AC: 611 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	11
DANN	Benign	0.39
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs17753394; hg19: chr22-38678387;