16-27366928-A-G

Variant names:

• chr16-27366928-A-G
• rs4787956

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 0.373 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
• Publications: 17 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.391 AC: 16214 AN: 41482

American (AMR) AF: 0.357 AC: 5453 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1041 AN: 3470

East Asian (EAS) AF: 0.555 AC: 2870 AN: 5172

South Asian (SAS) AF: 0.412 AC: 1986 AN: 4824

European-Finnish (FIN) AF: 0.366 AC: 3863 AN: 10568

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23852 AN: 67982

Other (OTH) AF: 0.345 AC: 728 AN: 2110

Alfa AF: 0.355 Hom.: 43240

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
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs4787956; hg19: chr16-27378249;