16-55709855-A-G

Variant names:

• chr16-55709855-A-G
• rs7188230

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 0.303 in 151,802 control chromosomes in the GnomAD database, including 8,891 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 0.30 (8891 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.814
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.303 AC: 45939 AN: 151682 Hom.: 8872 Cov.: 32

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.0299

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.303 AC: 46007 AN: 151802 Hom.: 8891 Cov.: 32 AF XY: 0.302 AC XY: 22438 AN XY: 74184

African (AFR) AF: 0.550 AC: 22766 AN: 41402

American (AMR) AF: 0.184 AC: 2807 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 814 AN: 3470

East Asian (EAS) AF: 0.0300 AC: 154 AN: 5136

South Asian (SAS) AF: 0.219 AC: 1051 AN: 4804

European-Finnish (FIN) AF: 0.272 AC: 2862 AN: 10536

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14641 AN: 67892

Other (OTH) AF: 0.273 AC: 574 AN: 2100

Alfa AF: 0.295 Hom.: 1524

Bravo AF: 0.306

Asia WGS AF: 0.146 AC: 510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.5
DANN	Benign	0.42
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs7188230; hg19: chr16-55743767;