rs223887

Variant names:

• chr16-57357302-G-T
• rs223887

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 0.675 in 148,730 control chromosomes in the GnomAD database, including 34,991 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 0.67 (34991 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.765 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: 0.675 AC: 100256 AN: 148616 Hom.: 34957 Cov.: 24

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.844

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.771

Gnomad OTH AF: 0.701

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

GnomAD4 genome AF: 0.675 AC: 100346 AN: 148730 Hom.: 34991 Cov.: 24 AF XY: 0.674 AC XY: 48826 AN XY: 72478

African (AFR) AF: 0.495 AC: 19706 AN: 39800

American (AMR) AF: 0.667 AC: 9961 AN: 14938

Ashkenazi Jewish (ASJ) AF: 0.768 AC: 2656 AN: 3460

East Asian (EAS) AF: 0.536 AC: 2698 AN: 5030

South Asian (SAS) AF: 0.534 AC: 2480 AN: 4644

European-Finnish (FIN) AF: 0.844 AC: 8506 AN: 10080

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.771 AC: 52046 AN: 67536

Other (OTH) AF: 0.705 AC: 1446 AN: 2050

Alfa AF: 0.725 Hom.: 5083

Bravo AF: 0.650

Asia WGS AF: 0.531 AC: 1850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.66
DANN	Benign	0.73
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs223887; hg19: chr16-57391214;