16-56959299-T-C

Position:

• chr16-56959299-T-C

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 0.176 in 152,166 control chromosomes in the GnomAD database, including 2,462 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 0.18 (2462 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.213 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: 0.177 AC: 26841 AN: 152048 Hom.: 2458 Cov.: 31

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.0710

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.176 AC: 26849 AN: 152166 Hom.: 2462 Cov.: 31 AF XY: 0.176 AC XY: 13088 AN XY: 74390

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.0708

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.190

Alfa AF: 0.184 Hom.: 460

Bravo AF: 0.175

Asia WGS AF: 0.144 AC: 502 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	2.9
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12708967; hg19: chr16-56993211;