16-56638468-C-G

Position:

• chr16-56638468-C-G

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 0.131 in 152,238 control chromosomes in the GnomAD database, including 1,331 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 0.13 (1331 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.219 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: 0.131 AC: 19857 AN: 152120 Hom.: 1327 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.131 AC: 19875 AN: 152238 Hom.: 1331 Cov.: 32 AF XY: 0.133 AC XY: 9924 AN XY: 74440

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.230

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.138

Alfa AF: 0.125 Hom.: 155

Bravo AF: 0.131

Asia WGS AF: 0.196 AC: 679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.7
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9922957; hg19: chr16-56672380;