16-22957589-T-C

Variant names:

• chr16-22957589-T-C
• rs208600

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 0.801 in 152,104 control chromosomes in the GnomAD database, including 49,136 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 0.80 (49136 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.816
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.892 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: 0.801 AC: 121691 AN: 151986 Hom.: 49069 Cov.: 31

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.828

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.785

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

GnomAD4 genome AF: 0.801 AC: 121822 AN: 152104 Hom.: 49136 Cov.: 31 AF XY: 0.804 AC XY: 59779 AN XY: 74358

African (AFR) AF: 0.899 AC: 37337 AN: 41512

American (AMR) AF: 0.827 AC: 12644 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.704 AC: 2444 AN: 3470

East Asian (EAS) AF: 0.828 AC: 4276 AN: 5164

South Asian (SAS) AF: 0.814 AC: 3930 AN: 4826

European-Finnish (FIN) AF: 0.803 AC: 8494 AN: 10576

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.737 AC: 50105 AN: 67954

Other (OTH) AF: 0.789 AC: 1664 AN: 2110

Alfa AF: 0.780 Hom.: 6031

Bravo AF: 0.807

Asia WGS AF: 0.837 AC: 2913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.5
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: rs208600; hg19: chr16-22968910;