16-56959299-T-C

Variant names:

• chr16-56959299-T-C
• rs12708967

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 0.176 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
• Publications: 23 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.157 AC: 6528 AN: 41492

American (AMR) AF: 0.200 AC: 3053 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 759 AN: 3470

East Asian (EAS) AF: 0.0708 AC: 366 AN: 5168

South Asian (SAS) AF: 0.224 AC: 1081 AN: 4822

European-Finnish (FIN) AF: 0.171 AC: 1811 AN: 10602

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12638 AN: 68010

Other (OTH) AF: 0.190 AC: 402 AN: 2112

Alfa AF: 0.180 Hom.: 536

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
PhyloP100		0.044

Splicing

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

Other links and lift over

dbSNP: rs12708967; hg19: chr16-56993211;