chr16-55199768-A-G

Variant names:

• chr16-55199768-A-G
• rs12926302

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 0.124 in 152,206 control chromosomes in the GnomAD database, including 1,215 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 0.12 (1215 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.504
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18883 AN: 152088 Hom.: 1216 Cov.: 33

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0853

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.0200

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0943

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.124 AC: 18883 AN: 152206 Hom.: 1215 Cov.: 33 AF XY: 0.122 AC XY: 9070 AN XY: 74394

African (AFR) AF: 0.169 AC: 7011 AN: 41508

American (AMR) AF: 0.0851 AC: 1301 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 399 AN: 3468

East Asian (EAS) AF: 0.0199 AC: 103 AN: 5176

South Asian (SAS) AF: 0.111 AC: 537 AN: 4822

European-Finnish (FIN) AF: 0.0943 AC: 1000 AN: 10600

Middle Eastern (MID) AF: 0.110 AC: 32 AN: 292

European-Non Finnish (NFE) AF: 0.121 AC: 8255 AN: 68020

Other (OTH) AF: 0.112 AC: 237 AN: 2116

Alfa AF: 0.104 Hom.: 485

Bravo AF: 0.126

Asia WGS AF: 0.0600 AC: 209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.54
DANN	Benign	0.73
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs12926302; hg19: chr16-55233680;