chr16-20083564-G-A

Variant names:

• chr16-20083564-G-A
• rs7185264

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 0.251 in 152,078 control chromosomes in the GnomAD database, including 4,831 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 0.25 (4831 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.257 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: 0.251 AC: 38127 AN: 151958 Hom.: 4830 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.251 AC: 38164 AN: 152078 Hom.: 4831 Cov.: 32 AF XY: 0.253 AC XY: 18787 AN XY: 74330

African (AFR) AF: 0.244 AC: 10123 AN: 41494

American (AMR) AF: 0.247 AC: 3778 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 721 AN: 3472

East Asian (EAS) AF: 0.269 AC: 1389 AN: 5170

South Asian (SAS) AF: 0.233 AC: 1120 AN: 4804

European-Finnish (FIN) AF: 0.300 AC: 3167 AN: 10562

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16955 AN: 67974

Other (OTH) AF: 0.233 AC: 492 AN: 2114

Alfa AF: 0.248 Hom.: 3685

Bravo AF: 0.249

Asia WGS AF: 0.239 AC: 829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.57
PhyloP100		0.098

Splicing

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

Other links and lift over

dbSNP: rs7185264; hg19: chr16-20094886;