16-31097388-C-G

Variant names:

• chr16-31097388-C-G
• rs17881535

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 0.164 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.164 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

Gnomad4 AFR AF: 0.0635

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.153

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.230

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.162

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17881535; hg19: chr16-31108709;