16-13811666-G-C

Variant names:

• chr16-13811666-G-C
• rs1002587

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 0.49 in 152,078 control chromosomes in the GnomAD database, including 23,013 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 0.49 (23013 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.879 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: 0.489 AC: 74371 AN: 151960 Hom.: 22942 Cov.: 32

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.490 AC: 74512 AN: 152078 Hom.: 23013 Cov.: 32 AF XY: 0.493 AC XY: 36675 AN XY: 74326

African (AFR) AF: 0.844 AC: 35034 AN: 41500

American (AMR) AF: 0.371 AC: 5659 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1232 AN: 3470

East Asian (EAS) AF: 0.901 AC: 4652 AN: 5166

South Asian (SAS) AF: 0.605 AC: 2919 AN: 4824

European-Finnish (FIN) AF: 0.307 AC: 3244 AN: 10560

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

European-Non Finnish (NFE) AF: 0.299 AC: 20338 AN: 67976

Other (OTH) AF: 0.451 AC: 952 AN: 2112

Alfa AF: 0.391 Hom.: 1955

Bravo AF: 0.509

Asia WGS AF: 0.790 AC: 2746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.5
DANN	Benign	0.49
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs1002587; hg19: chr16-13905523;