16-52550383-T-G

Position:

• chr16-52550383-T-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.367 in 152,136 control chromosomes in the GnomAD database, including 11,293 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 0.37 (11293 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.99

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.603 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: 0.367 AC: 55800 AN: 152018 Hom.: 11260 Cov.: 33

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.367 AC: 55898 AN: 152136 Hom.: 11293 Cov.: 33 AF XY: 0.370 AC XY: 27526 AN XY: 74372

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.384

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.620

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.363

Alfa AF: 0.313 Hom.: 2270

Bravo AF: 0.383

Asia WGS AF: 0.434 AC: 1509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	19
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3095607; hg19: chr16-52584295;