rs16899168

Variant names:

• chr6-31290910-G-A
• rs16899168

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 0.0485 in 152,162 control chromosomes in the GnomAD database, including 298 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 0.049 (298 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.64

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.144 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: 0.0485 AC: 7376 AN: 152044 Hom.: 295 Cov.: 32

Gnomad AFR AF: 0.0378

Gnomad AMI AF: 0.00549

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.0271

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.0472

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0285

Gnomad OTH AF: 0.0507

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

GnomAD4 genome AF: 0.0485 AC: 7380 AN: 152162 Hom.: 298 Cov.: 32 AF XY: 0.0532 AC XY: 3960 AN XY: 74370

Gnomad4 AFR AF: 0.0376

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.0271

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.0472

Gnomad4 NFE AF: 0.0285

Gnomad4 OTH AF: 0.0507

Alfa AF: 0.0426 Hom.: 68

Bravo AF: 0.0521

Asia WGS AF: 0.153 AC: 530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.083
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16899168; hg19: chr6-31258687;