rs10221083

Variant names:

• chr16-84201134-A-G
• rs10221083

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 0.32 in 152,202 control chromosomes in the GnomAD database, including 7,916 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 0.32 (7916 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.85
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.354 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: 0.320 AC: 48714 AN: 152084 Hom.: 7908 Cov.: 33

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.320 AC: 48751 AN: 152202 Hom.: 7916 Cov.: 33 AF XY: 0.324 AC XY: 24128 AN XY: 74414

African (AFR) AF: 0.359 AC: 14896 AN: 41502

American (AMR) AF: 0.330 AC: 5047 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1131 AN: 3468

East Asian (EAS) AF: 0.329 AC: 1704 AN: 5186

South Asian (SAS) AF: 0.327 AC: 1579 AN: 4830

European-Finnish (FIN) AF: 0.333 AC: 3530 AN: 10600

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19933 AN: 68004

Other (OTH) AF: 0.282 AC: 597 AN: 2114

Alfa AF: 0.300 Hom.: 8606

Bravo AF: 0.325

Asia WGS AF: 0.299 AC: 1040 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.018
DANN	Benign	0.44
PhyloP100		-4.8

Splicing

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

Other links and lift over

dbSNP: rs10221083; hg19: chr16-84234740;