rs1859308

Variant names:

• chr16-27386677-A-G
• rs1859308

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 0.877 in 152,036 control chromosomes in the GnomAD database, including 58,727 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 0.88 (58727 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.416
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.937 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: 0.877 AC: 133227 AN: 151918 Hom.: 58674 Cov.: 30

Gnomad AFR AF: 0.945

Gnomad AMI AF: 0.809

Gnomad AMR AF: 0.863

Gnomad ASJ AF: 0.845

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.862

Gnomad OTH AF: 0.862

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

GnomAD4 genome AF: 0.877 AC: 133337 AN: 152036 Hom.: 58727 Cov.: 30 AF XY: 0.876 AC XY: 65078 AN XY: 74314

African (AFR) AF: 0.945 AC: 39188 AN: 41478

American (AMR) AF: 0.863 AC: 13182 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.845 AC: 2932 AN: 3468

East Asian (EAS) AF: 0.672 AC: 3458 AN: 5146

South Asian (SAS) AF: 0.870 AC: 4185 AN: 4808

European-Finnish (FIN) AF: 0.847 AC: 8936 AN: 10544

Middle Eastern (MID) AF: 0.901 AC: 263 AN: 292

European-Non Finnish (NFE) AF: 0.862 AC: 58632 AN: 68000

Other (OTH) AF: 0.862 AC: 1823 AN: 2114

Alfa AF: 0.865 Hom.: 251968

Bravo AF: 0.877

Asia WGS AF: 0.794 AC: 2761 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.5
DANN	Benign	0.68
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs1859308; hg19: chr16-27397998;