rs17826681

Positions:

• chr8-57853913-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 0.0903 in 152,078 control chromosomes in the GnomAD database, including 780 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 0.090 (780 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.366

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.126 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: 0.0904 AC: 13730 AN: 151960 Hom.: 780 Cov.: 32

Gnomad AFR AF: 0.0396

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.0599

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.0630

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.0851

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

GnomAD4 genome AF: 0.0903 AC: 13739 AN: 152078 Hom.: 780 Cov.: 32 AF XY: 0.0892 AC XY: 6633 AN XY: 74330

Gnomad4 AFR AF: 0.0400

Gnomad4 AMR AF: 0.0599

Gnomad4 ASJ AF: 0.134

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.0629

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.0842

Alfa AF: 0.119 Hom.: 1700

Bravo AF: 0.0826

Asia WGS AF: 0.0360 AC: 125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17826681; hg19: chr8-58766472;