chr16-31097388-C-G

Variant names:

• chr16-31097388-C-G
• rs17881535

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 0.164 in 152,056 control chromosomes in the GnomAD database, including 2,538 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 0.16 (2538 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.204
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24942 AN: 151938 Hom.: 2538 Cov.: 32

Gnomad AFR AF: 0.0635

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.164 AC: 24943 AN: 152056 Hom.: 2538 Cov.: 32 AF XY: 0.162 AC XY: 12055 AN XY: 74346

African (AFR) AF: 0.0635 AC: 2633 AN: 41494

American (AMR) AF: 0.161 AC: 2461 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 530 AN: 3472

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5168

South Asian (SAS) AF: 0.106 AC: 511 AN: 4826

European-Finnish (FIN) AF: 0.230 AC: 2434 AN: 10578

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15794 AN: 67956

Other (OTH) AF: 0.162 AC: 343 AN: 2114

Alfa AF: 0.0852 Hom.: 120

Bravo AF: 0.152

Asia WGS AF: 0.0550 AC: 191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.38
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs17881535; hg19: chr16-31108709;