rs17880887

Variant names:

• chr16-31099180-G-T
• rs17880887

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.23 in 151,850 control chromosomes in the GnomAD database, including 5,069 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 0.23 (5069 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.336 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: 0.231 AC: 34994 AN: 151728 Hom.: 5069 Cov.: 31

Gnomad AFR AF: 0.0821

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.00156

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.230 AC: 34992 AN: 151850 Hom.: 5069 Cov.: 31 AF XY: 0.226 AC XY: 16773 AN XY: 74218

Gnomad4 AFR AF: 0.0820

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.00156

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.222

Alfa AF: 0.205 Hom.: 832

Bravo AF: 0.216

Asia WGS AF: 0.0710 AC: 246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	1.8
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17880887; hg19: chr16-31110501;