rs16893526

Variant names:

• chr6-81805598-G-A
• rs16893526

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 0.0824 in 151,894 control chromosomes in the GnomAD database, including 582 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 0.082 (582 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.698

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 (EAS) 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: 0.0824 AC: 12508 AN: 151776 Hom.: 583 Cov.: 32

Gnomad AFR AF: 0.0867

Gnomad AMI AF: 0.0758

Gnomad AMR AF: 0.0670

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.0985

Gnomad FIN AF: 0.0249

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0830

Gnomad OTH AF: 0.0984

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

GnomAD4 genome AF: 0.0824 AC: 12513 AN: 151894 Hom.: 582 Cov.: 32 AF XY: 0.0802 AC XY: 5953 AN XY: 74252

Gnomad4 AFR AF: 0.0866

Gnomad4 AMR AF: 0.0668

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.0992

Gnomad4 FIN AF: 0.0249

Gnomad4 NFE AF: 0.0830

Gnomad4 OTH AF: 0.0973

Alfa AF: 0.0883 Hom.: 1177

Bravo AF: 0.0864

Asia WGS AF: 0.115 AC: 399 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.17
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16893526; hg19: chr6-82515315;