chr16-60698027-A-C

Variant names:

• chr16-60698027-A-C
• rs2059252

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 0.936 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
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• 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

African (AFR) AF: 0.960 AC: 39895 AN: 41572

American (AMR) AF: 0.943 AC: 14418 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.919 AC: 3192 AN: 3472

East Asian (EAS) AF: 0.944 AC: 4890 AN: 5178

South Asian (SAS) AF: 0.948 AC: 4571 AN: 4822

European-Finnish (FIN) AF: 0.955 AC: 10136 AN: 10610

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.916 AC: 62339 AN: 68034

Other (OTH) AF: 0.929 AC: 1963 AN: 2112

Alfa AF: 0.919 Hom.: 3349

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
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs2059252; hg19: chr16-60731931;