16-20356368-G-T

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 0.137 in 152,638 control chromosomes in the GnomAD database, including 1,791 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 0.14 (1788 hom., cov: 32)
  • Exomes 𝑓: 0.081 (3 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.24

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.177 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: 0.138 AC: 20935 AN: 152114 Hom.: 1786 Cov.: 32

Gnomad AFR AF: 0.0465

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.0112

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.149

GnomAD4 exome AF: 0.0813 AC: 33 AN: 406 Hom.: 3 AF XY: 0.0940 AC XY: 22 AN XY: 234

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.214

Gnomad4 NFE exome AF: 0.0865

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.138 AC: 20937 AN: 152232 Hom.: 1788 Cov.: 32 AF XY: 0.139 AC XY: 10341 AN XY: 74428

Gnomad4 AFR AF: 0.0465

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.0108

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.151

Alfa AF: 0.157 Hom.: 2464

Bravo AF: 0.129

Asia WGS AF: 0.0850 AC: 294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
Cadd	Benign	19
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12917707; hg19: chr16-20367690;