rs2059251

Variant names:

• chr16-60696886-T-A
• rs2059251

Your query was ambiguous. Multiple possible variants found:

• chr16-60696886-T-A
• chr16-60696886-T-C

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 0.411 in 152,000 control chromosomes in the GnomAD database, including 13,833 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 0.41 (13833 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.815
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.494 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: 0.411 AC: 62427 AN: 151882 Hom.: 13837 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.0972

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.411 AC: 62444 AN: 152000 Hom.: 13833 Cov.: 32 AF XY: 0.408 AC XY: 30311 AN XY: 74292

African (AFR) AF: 0.297 AC: 12301 AN: 41440

American (AMR) AF: 0.361 AC: 5522 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1814 AN: 3470

East Asian (EAS) AF: 0.0968 AC: 501 AN: 5174

South Asian (SAS) AF: 0.327 AC: 1574 AN: 4818

European-Finnish (FIN) AF: 0.511 AC: 5396 AN: 10562

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33887 AN: 67952

Other (OTH) AF: 0.414 AC: 872 AN: 2108

Alfa AF: 0.307 Hom.: 799

Bravo AF: 0.395

Asia WGS AF: 0.213 AC: 745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.2
DANN	Benign	0.77
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs2059251; hg19: chr16-60730790;