16-27366928-A-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 0.373 in 152,088 control chromosomes in the GnomAD database, including 10,730 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 0.37 (10730 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.538 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: 0.373 AC: 56635 AN: 151970 Hom.: 10719 Cov.: 32

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.373 AC: 56678 AN: 152088 Hom.: 10730 Cov.: 32 AF XY: 0.375 AC XY: 27896 AN XY: 74324

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.357

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.555

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.345

Alfa AF: 0.350 Hom.: 19486

Bravo AF: 0.375

Asia WGS AF: 0.455 AC: 1585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.44
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4787956; hg19: chr16-27378249;