16-22993770-G-T

Variant names:

• chr16-22993770-G-T
• rs16975343

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 0.0841 in 152,178 control chromosomes in the GnomAD database, including 675 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 0.084 (675 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.741
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.133 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: 0.0838 AC: 12745 AN: 152060 Hom.: 658 Cov.: 31

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0474

Gnomad ASJ AF: 0.0349

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.0313

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0735

Gnomad OTH AF: 0.0654

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

GnomAD4 genome AF: 0.0841 AC: 12799 AN: 152178 Hom.: 675 Cov.: 31 AF XY: 0.0838 AC XY: 6237 AN XY: 74400

African (AFR) AF: 0.116 AC: 4802 AN: 41514

American (AMR) AF: 0.0473 AC: 723 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0349 AC: 121 AN: 3472

East Asian (EAS) AF: 0.141 AC: 729 AN: 5156

South Asian (SAS) AF: 0.0307 AC: 148 AN: 4820

European-Finnish (FIN) AF: 0.104 AC: 1101 AN: 10608

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0735 AC: 4998 AN: 67994

Other (OTH) AF: 0.0652 AC: 138 AN: 2116

Alfa AF: 0.0739 Hom.: 255

Bravo AF: 0.0813

Asia WGS AF: 0.0970 AC: 337 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	0.23
DANN	Benign	0.16
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs16975343; hg19: chr16-23005091;