rs366542

Variant names:

• chr22-17775616-C-T
• rs366542

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 0.636 in 152,040 control chromosomes in the GnomAD database, including 32,806 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 0.64 (32806 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.882 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: 0.635 AC: 96546 AN: 151922 Hom.: 32757 Cov.: 32

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.636 AC: 96658 AN: 152040 Hom.: 32806 Cov.: 32 AF XY: 0.635 AC XY: 47190 AN XY: 74318

African (AFR) AF: 0.890 AC: 36926 AN: 41494

American (AMR) AF: 0.595 AC: 9095 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1814 AN: 3470

East Asian (EAS) AF: 0.513 AC: 2642 AN: 5154

South Asian (SAS) AF: 0.675 AC: 3251 AN: 4816

European-Finnish (FIN) AF: 0.534 AC: 5645 AN: 10576

Middle Eastern (MID) AF: 0.493 AC: 144 AN: 292

European-Non Finnish (NFE) AF: 0.520 AC: 35354 AN: 67942

Other (OTH) AF: 0.571 AC: 1205 AN: 2112

Alfa AF: 0.553 Hom.: 45258

Bravo AF: 0.648

Asia WGS AF: 0.623 AC: 2170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.24
DANN	Benign	0.42
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs366542; hg19: chr22-18258382;