rs10521114

Variant names:

• chr16-20078432-G-A
• rs10521114

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 0.252 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.696
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.251 AC: 10419 AN: 41470

American (AMR) AF: 0.248 AC: 3787 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 638 AN: 3472

East Asian (EAS) AF: 0.259 AC: 1332 AN: 5142

South Asian (SAS) AF: 0.232 AC: 1120 AN: 4818

European-Finnish (FIN) AF: 0.297 AC: 3139 AN: 10566

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16917 AN: 67962

Other (OTH) AF: 0.229 AC: 483 AN: 2108

Alfa AF: 0.249 Hom.: 3950

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
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs10521114; hg19: chr16-20089754;