chr16-55211125-G-A

Variant names:

• chr16-55211125-G-A
• rs17291845

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 0.108 in 152,172 control chromosomes in the GnomAD database, including 907 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 0.11 (907 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.381
• Publications: 12 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 (NFE) allele frequency at 95% confidence interval = 0.132 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: 0.108 AC: 16478 AN: 152054 Hom.: 904 Cov.: 33

Gnomad AFR AF: 0.0885

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0811

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.0230

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.108 AC: 16483 AN: 152172 Hom.: 907 Cov.: 33 AF XY: 0.106 AC XY: 7915 AN XY: 74394

African (AFR) AF: 0.0887 AC: 3682 AN: 41514

American (AMR) AF: 0.0809 AC: 1237 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 397 AN: 3472

East Asian (EAS) AF: 0.0229 AC: 118 AN: 5164

South Asian (SAS) AF: 0.114 AC: 550 AN: 4820

European-Finnish (FIN) AF: 0.107 AC: 1132 AN: 10602

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9101 AN: 67992

Other (OTH) AF: 0.106 AC: 224 AN: 2112

Alfa AF: 0.123 Hom.: 5462

Bravo AF: 0.106

Asia WGS AF: 0.0600 AC: 207 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	1.1
DANN	Benign	0.47
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs17291845; hg19: chr16-55245037;