16-20079323-G-A

Variant names:

• chr16-20079323-G-A
• rs10521115

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 0.219 in 151,914 control chromosomes in the GnomAD database, including 3,871 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 0.22 (3871 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.247 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: 0.219 AC: 33308 AN: 151796 Hom.: 3871 Cov.: 31

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.219 AC: 33332 AN: 151914 Hom.: 3871 Cov.: 31 AF XY: 0.222 AC XY: 16498 AN XY: 74250

African (AFR) AF: 0.141 AC: 5832 AN: 41432

American (AMR) AF: 0.234 AC: 3574 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 612 AN: 3466

East Asian (EAS) AF: 0.259 AC: 1333 AN: 5148

South Asian (SAS) AF: 0.231 AC: 1111 AN: 4800

European-Finnish (FIN) AF: 0.297 AC: 3128 AN: 10548

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16884 AN: 67940

Other (OTH) AF: 0.209 AC: 442 AN: 2114

Alfa AF: 0.232 Hom.: 5777

Bravo AF: 0.213

Asia WGS AF: 0.231 AC: 800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.5
DANN	Benign	0.80
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs10521115; hg19: chr16-20090645;