16-55211125-G-A

Position:

• chr16-55211125-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.0887

Gnomad4 AMR AF: 0.0809

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.0229

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.106

Alfa AF: 0.125 Hom.: 2816

Bravo AF: 0.106

Asia WGS AF: 0.0600 AC: 207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17291845; hg19: chr16-55245037;