rs16881502

Positions:

• chr6-18933188-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 0.0914 in 151,902 control chromosomes in the GnomAD database, including 1,691 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 0.091 (1691 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0913 AC: 13852 AN: 151782 Hom.: 1686 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0567

Gnomad ASJ AF: 0.00837

Gnomad EAS AF: 0.00117

Gnomad SAS AF: 0.00997

Gnomad FIN AF: 0.0258

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0155

Gnomad OTH AF: 0.0663

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

GnomAD4 genome AF: 0.0914 AC: 13890 AN: 151902 Hom.: 1691 Cov.: 32 AF XY: 0.0892 AC XY: 6622 AN XY: 74246

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.0567

Gnomad4 ASJ AF: 0.00837

Gnomad4 EAS AF: 0.00117

Gnomad4 SAS AF: 0.00998

Gnomad4 FIN AF: 0.0258

Gnomad4 NFE AF: 0.0155

Gnomad4 OTH AF: 0.0656

Alfa AF: 0.0290 Hom.: 382

Bravo AF: 0.103

Asia WGS AF: 0.0250 AC: 87 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16881502; hg19: chr6-18933419;