16-84200625-T-C

Variant names:

• chr16-84200625-T-C
• rs8051159

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 0.382 in 152,050 control chromosomes in the GnomAD database, including 11,096 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 0.38 (11096 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.884
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57955 AN: 151932 Hom.: 11078 Cov.: 33

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.382 AC: 58009 AN: 152050 Hom.: 11096 Cov.: 33 AF XY: 0.384 AC XY: 28572 AN XY: 74336

African (AFR) AF: 0.400 AC: 16566 AN: 41440

American (AMR) AF: 0.353 AC: 5397 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1546 AN: 3468

East Asian (EAS) AF: 0.339 AC: 1751 AN: 5166

South Asian (SAS) AF: 0.508 AC: 2445 AN: 4816

European-Finnish (FIN) AF: 0.347 AC: 3671 AN: 10592

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.375 AC: 25473 AN: 67964

Other (OTH) AF: 0.366 AC: 774 AN: 2112

Alfa AF: 0.375 Hom.: 18543

Bravo AF: 0.379

Asia WGS AF: 0.431 AC: 1499 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.7
DANN	Benign	0.55
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs8051159; hg19: chr16-84234231;