16-55268359-G-A

Position:

• chr16-55268359-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 0.153 in 152,062 control chromosomes in the GnomAD database, including 2,032 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 0.15 (2032 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.55268359G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000259283	ENST00000558730.2	n.216-1565C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23182 AN: 151944 Hom.: 2014 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.0846

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.153 AC: 23238 AN: 152062 Hom.: 2032 Cov.: 32 AF XY: 0.152 AC XY: 11312 AN XY: 74338

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.306

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.164

Alfa AF: 0.146 Hom.: 321

Bravo AF: 0.167

Asia WGS AF: 0.249 AC: 862 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.94
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4567706; hg19: chr16-55302271;