rs10521114

Positions:

• chr16-20078432-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 0.252 in 152,026 control chromosomes in the GnomAD database, including 4,819 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 0.25 (4819 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.696

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.20078432G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38215 AN: 151908 Hom.: 4815 Cov.: 31

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.252 AC: 38251 AN: 152026 Hom.: 4819 Cov.: 31 AF XY: 0.254 AC XY: 18867 AN XY: 74318

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.229

Alfa AF: 0.252 Hom.: 1620

Bravo AF: 0.251

Asia WGS AF: 0.236 AC: 818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.94
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521114; hg19: chr16-20089754;