16-53522178-C-T

Position:

• chr16-53522178-C-T

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 0.436 in 151,892 control chromosomes in the GnomAD database, including 15,938 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 0.44 (15938 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.647

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 (AFR) allele frequency at 95% confidence interval = 0.629 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: 0.436 AC: 66190 AN: 151774 Hom.: 15893 Cov.: 30

Gnomad AFR AF: 0.635

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.436 AC: 66300 AN: 151892 Hom.: 15938 Cov.: 30 AF XY: 0.433 AC XY: 32142 AN XY: 74244

Gnomad4 AFR AF: 0.636

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.502

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.436

Alfa AF: 0.402 Hom.: 4734

Bravo AF: 0.459

Asia WGS AF: 0.519 AC: 1806 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	3.9
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11863156; hg19: chr16-53556090;