16-52423230-A-G

Position:

• chr16-52423230-A-G

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 0.507 in 151,908 control chromosomes in the GnomAD database, including 21,592 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 0.51 (21592 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.104

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.507 AC: 76913 AN: 151790 Hom.: 21559 Cov.: 32

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.803

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.507 AC: 76993 AN: 151908 Hom.: 21592 Cov.: 32 AF XY: 0.512 AC XY: 38016 AN XY: 74210

Gnomad4 AFR AF: 0.728

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.802

Gnomad4 SAS AF: 0.573

Gnomad4 FIN AF: 0.407

Gnomad4 NFE AF: 0.373

Gnomad4 OTH AF: 0.490

Alfa AF: 0.399 Hom.: 17677

Bravo AF: 0.524

Asia WGS AF: 0.672 AC: 2336 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	3.4
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8049226; hg19: chr16-52457142;