rs2059252

Variant names:

• chr16-60698027-A-C
• rs2059252

Your query was ambiguous. Multiple possible variants found:

• chr16-60698027-A-C
• chr16-60698027-A-G
• chr16-60698027-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 0.936 in 152,296 control chromosomes in the GnomAD database, including 66,746 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 0.94 (66746 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02

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 (AFR) allele frequency at 95% confidence interval = 0.952 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: 0.936 AC: 142428 AN: 152178 Hom.: 66691 Cov.: 32

Gnomad AFR AF: 0.960

Gnomad AMI AF: 0.954

Gnomad AMR AF: 0.943

Gnomad ASJ AF: 0.919

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.948

Gnomad FIN AF: 0.955

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.916

Gnomad OTH AF: 0.928

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

GnomAD4 genome AF: 0.936 AC: 142542 AN: 152296 Hom.: 66746 Cov.: 32 AF XY: 0.938 AC XY: 69859 AN XY: 74456

Gnomad4 AFR AF: 0.960

Gnomad4 AMR AF: 0.943

Gnomad4 ASJ AF: 0.919

Gnomad4 EAS AF: 0.944

Gnomad4 SAS AF: 0.948

Gnomad4 FIN AF: 0.955

Gnomad4 NFE AF: 0.916

Gnomad4 OTH AF: 0.929

Alfa AF: 0.914 Hom.: 2989

Bravo AF: 0.936

Asia WGS AF: 0.939 AC: 3266 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	0.24
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2059252; hg19: chr16-60731931;