rs16881502

Variant names:

• chr6-18933188-A-G
• rs16881502

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 0.0914 in 151,902 control chromosomes in the GnomAD database, including 1,691 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 0.091 (1691 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0913 AC: 13852 AN: 151782 Hom.: 1686 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0567

Gnomad ASJ AF: 0.00837

Gnomad EAS AF: 0.00117

Gnomad SAS AF: 0.00997

Gnomad FIN AF: 0.0258

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0155

Gnomad OTH AF: 0.0663

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

GnomAD4 genome AF: 0.0914 AC: 13890 AN: 151902 Hom.: 1691 Cov.: 32 AF XY: 0.0892 AC XY: 6622 AN XY: 74246

African (AFR) AF: 0.277 AC: 11472 AN: 41438

American (AMR) AF: 0.0567 AC: 864 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.00837 AC: 29 AN: 3466

East Asian (EAS) AF: 0.00117 AC: 6 AN: 5122

South Asian (SAS) AF: 0.00998 AC: 48 AN: 4810

European-Finnish (FIN) AF: 0.0258 AC: 274 AN: 10608

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0155 AC: 1054 AN: 67916

Other (OTH) AF: 0.0656 AC: 138 AN: 2104

Alfa AF: 0.0374 Hom.: 726

Bravo AF: 0.103

Asia WGS AF: 0.0250 AC: 87 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.53
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs16881502; hg19: chr6-18933419;