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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.892

Gnomad4 AMR AF: 0.907

Gnomad4 ASJ AF: 0.906

Gnomad4 EAS AF: 0.944

Gnomad4 SAS AF: 0.921

Gnomad4 FIN AF: 0.842

Gnomad4 NFE AF: 0.827

Gnomad4 OTH AF: 0.878

Alfa AF: 0.842 Hom.: 51700

Bravo AF: 0.871

Asia WGS AF: 0.938 AC: 3263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.7
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4888201; hg19: chr16-82000020;