16-22681003-C-T

Variant names:

• chr16-22681003-C-T
• rs251837

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 0.842 in 152,216 control chromosomes in the GnomAD database, including 52,206 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 0.84 (52206 hom., cov: 63)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.913 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: 0.842 AC: 128016 AN: 152098 Hom.: 52156 Cov.: 63

Gnomad AFR AF: 0.921

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.881

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.841

Gnomad OTH AF: 0.810

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

GnomAD4 genome AF: 0.842 AC: 128126 AN: 152216 Hom.: 52206 Cov.: 63 AF XY: 0.838 AC XY: 62343 AN XY: 74430

African (AFR) AF: 0.921 AC: 38287 AN: 41568

American (AMR) AF: 0.726 AC: 11094 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.766 AC: 2658 AN: 3470

East Asian (EAS) AF: 0.602 AC: 3102 AN: 5152

South Asian (SAS) AF: 0.791 AC: 3812 AN: 4818

European-Finnish (FIN) AF: 0.881 AC: 9348 AN: 10612

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.841 AC: 57192 AN: 68004

Other (OTH) AF: 0.810 AC: 1714 AN: 2116

Alfa AF: 0.845 Hom.: 5655

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.16
DANN	Benign	0.36
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs251837; hg19: chr16-22692324;