rs4888201

Variant names:

• chr16-81966415-A-G
• rs4888201

Your query was ambiguous. Multiple possible variants found:

• chr16-81966415-A-G
• chr16-81966415-A-T

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 0.863 in 152,144 control chromosomes in the GnomAD database, including 56,857 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 0.86 (56857 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660
• Publications: 5 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 = 0.922 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: 0.863 AC: 131249 AN: 152026 Hom.: 56804 Cov.: 31

Gnomad AFR AF: 0.892

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.906

Gnomad ASJ AF: 0.906

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.921

Gnomad FIN AF: 0.842

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.879

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

GnomAD4 genome AF: 0.863 AC: 131362 AN: 152144 Hom.: 56857 Cov.: 31 AF XY: 0.866 AC XY: 64402 AN XY: 74382

African (AFR) AF: 0.892 AC: 37024 AN: 41490

American (AMR) AF: 0.907 AC: 13864 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.906 AC: 3145 AN: 3470

East Asian (EAS) AF: 0.944 AC: 4897 AN: 5188

South Asian (SAS) AF: 0.921 AC: 4436 AN: 4818

European-Finnish (FIN) AF: 0.842 AC: 8902 AN: 10568

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.827 AC: 56239 AN: 68002

Other (OTH) AF: 0.878 AC: 1855 AN: 2112

Alfa AF: 0.845 Hom.: 70263

Bravo AF: 0.871

Asia WGS AF: 0.938 AC: 3263 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	1.7
DANN	Benign	0.57
PhyloP100		-0.066

Splicing

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

Other links and lift over

dbSNP: rs4888201; hg19: chr16-82000020;