rs6498017

chr16-27383537-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;