16-27399508-A-G

Variant names:

• chr16-27399508-A-G
• rs2107357

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 0.848 in 152,260 control chromosomes in the GnomAD database, including 54,859 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 0.85 (54859 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.31
• Publications: 18 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.848 AC: 129018 AN: 152142 Hom.: 54827 Cov.: 33

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.849

Gnomad ASJ AF: 0.838

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.909

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.864

Gnomad OTH AF: 0.848

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

GnomAD4 genome AF: 0.848 AC: 129100 AN: 152260 Hom.: 54859 Cov.: 33 AF XY: 0.851 AC XY: 63335 AN XY: 74442

African (AFR) AF: 0.823 AC: 34187 AN: 41560

American (AMR) AF: 0.849 AC: 12978 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.838 AC: 2908 AN: 3472

East Asian (EAS) AF: 0.696 AC: 3597 AN: 5168

South Asian (SAS) AF: 0.871 AC: 4203 AN: 4826

European-Finnish (FIN) AF: 0.909 AC: 9646 AN: 10612

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.864 AC: 58788 AN: 68010

Other (OTH) AF: 0.848 AC: 1793 AN: 2114

Alfa AF: 0.862 Hom.: 14600

Bravo AF: 0.838

Asia WGS AF: 0.810 AC: 2816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0020
DANN	Benign	0.29
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs2107357; hg19: chr16-27410829;