chr16-56959412-C-A

Position:

• chr16-56959412-C-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 0.31 in 152,014 control chromosomes in the GnomAD database, including 7,506 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

• Frequency: Genomes: 𝑓 0.31 (7506 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: -0.826

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.322 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: 0.310 AC: 47073 AN: 151896 Hom.: 7489 Cov.: 31

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.310 AC: 47124 AN: 152014 Hom.: 7506 Cov.: 31 AF XY: 0.308 AC XY: 22898 AN XY: 74302

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.279

Alfa AF: 0.317 Hom.: 17009

Bravo AF: 0.310

Asia WGS AF: 0.228 AC: 797 AN: 3478

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

Submissions by phenotype

not provided Other:1

not provided, no classification provided

not provided

Department of Ophthalmology and Visual Sciences Kyoto University

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.75
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3764261; hg19: chr16-56993324;