rs6498017

Variant names:

• chr16-27383537-A-G
• rs6498017

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 0.882 in 152,236 control chromosomes in the GnomAD database, including 59,483 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 0.88 (59483 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.182

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 = 0.953 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: 0.882 AC: 134114 AN: 152118 Hom.: 59429 Cov.: 32

Gnomad AFR AF: 0.961

Gnomad AMI AF: 0.809

Gnomad AMR AF: 0.864

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.870

Gnomad FIN AF: 0.848

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.862

Gnomad OTH AF: 0.868

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

GnomAD4 genome AF: 0.882 AC: 134225 AN: 152236 Hom.: 59483 Cov.: 32 AF XY: 0.880 AC XY: 65515 AN XY: 74418

Gnomad4 AFR AF: 0.961

Gnomad4 AMR AF: 0.864

Gnomad4 ASJ AF: 0.846

Gnomad4 EAS AF: 0.673

Gnomad4 SAS AF: 0.870

Gnomad4 FIN AF: 0.848

Gnomad4 NFE AF: 0.862

Gnomad4 OTH AF: 0.868

Alfa AF: 0.878 Hom.: 9564

Bravo AF: 0.882

Asia WGS AF: 0.795 AC: 2765 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	2.7
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6498017; hg19: chr16-27394858;