16-56959412-C-A

Variant names:

• chr16-56959412-C-A
• rs3764261

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 0.31 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
• Publications: 387 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.321 AC: 13321 AN: 41462

American (AMR) AF: 0.295 AC: 4501 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 882 AN: 3472

East Asian (EAS) AF: 0.165 AC: 853 AN: 5170

South Asian (SAS) AF: 0.335 AC: 1610 AN: 4804

European-Finnish (FIN) AF: 0.276 AC: 2919 AN: 10558

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 22019 AN: 67966

Other (OTH) AF: 0.279 AC: 589 AN: 2110

Alfa AF: 0.316 Hom.: 34712

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

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Department of Ophthalmology and Visual Sciences Kyoto University

Significance: not provided

Review Status: no classification provided

Collection Method: not provided

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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
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs3764261; hg19: chr16-56993324;