rs2059252

chr16-60698027-A-Cchr16-60698027-A-Gchr16-60698027-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;