16-69520978-G-A

Variant names:

• chr16-69520978-G-A
• rs12921716

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 0.0579 in 152,226 control chromosomes in the GnomAD database, including 399 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 0.058 (399 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0862 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: 0.0580 AC: 8817 AN: 152108 Hom.: 399 Cov.: 32

Gnomad AFR AF: 0.0139

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.0469

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0278

Gnomad FIN AF: 0.0732

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0881

Gnomad OTH AF: 0.0670

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

GnomAD4 genome AF: 0.0579 AC: 8813 AN: 152226 Hom.: 399 Cov.: 32 AF XY: 0.0567 AC XY: 4217 AN XY: 74424

African (AFR) AF: 0.0139 AC: 578 AN: 41562

American (AMR) AF: 0.0468 AC: 716 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 372 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5178

South Asian (SAS) AF: 0.0278 AC: 134 AN: 4824

European-Finnish (FIN) AF: 0.0732 AC: 775 AN: 10588

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0881 AC: 5989 AN: 68002

Other (OTH) AF: 0.0664 AC: 140 AN: 2110

Alfa AF: 0.0722 Hom.: 354

Bravo AF: 0.0546

Asia WGS AF: 0.0130 AC: 45 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	11
DANN	Benign	0.77
PhyloP100		0.058

Splicing

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

Other links and lift over

dbSNP: rs12921716; hg19: chr16-69554881;