16-20084306-A-C

Variant names:

• chr16-20084306-A-C
• rs11647507

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 0.22 in 152,164 control chromosomes in the GnomAD database, including 3,897 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 (3897 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.255 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: 0.220 AC: 33428 AN: 152044 Hom.: 3897 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.220 AC: 33449 AN: 152164 Hom.: 3897 Cov.: 32 AF XY: 0.223 AC XY: 16561 AN XY: 74396

African (AFR) AF: 0.140 AC: 5822 AN: 41538

American (AMR) AF: 0.234 AC: 3577 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 613 AN: 3466

East Asian (EAS) AF: 0.266 AC: 1376 AN: 5164

South Asian (SAS) AF: 0.233 AC: 1121 AN: 4820

European-Finnish (FIN) AF: 0.299 AC: 3169 AN: 10584

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

European-Non Finnish (NFE) AF: 0.249 AC: 16913 AN: 67990

Other (OTH) AF: 0.210 AC: 444 AN: 2116

Alfa AF: 0.232 Hom.: 7225

Bravo AF: 0.214

Asia WGS AF: 0.234 AC: 809 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.0020
DANN	Benign	0.59
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs11647507; hg19: chr16-20095628;