rs6498016

Variant names:

• chr16-27380467-G-A
• rs6498016

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 0.19 in 152,220 control chromosomes in the GnomAD database, including 2,810 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 0.19 (2810 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.212 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: 0.190 AC: 28962 AN: 152102 Hom.: 2810 Cov.: 33

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.0513

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.190 AC: 28977 AN: 152220 Hom.: 2810 Cov.: 33 AF XY: 0.188 AC XY: 14000 AN XY: 74408

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.0520

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.172

Alfa AF: 0.182 Hom.: 5408

Bravo AF: 0.186

Asia WGS AF: 0.104 AC: 360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.6
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6498016; hg19: chr16-27391788; COSMIC: COSV69964755;