rs17057381

Positions:

• chr8-27559284-G-A

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 0.0464 in 152,260 control chromosomes in the GnomAD database, including 298 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 0.046 (298 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.286

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.109 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: 0.0463 AC: 7051 AN: 152142 Hom.: 297 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0264

Gnomad ASJ AF: 0.0375

Gnomad EAS AF: 0.0116

Gnomad SAS AF: 0.0612

Gnomad FIN AF: 0.00188

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0205

Gnomad OTH AF: 0.0463

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

GnomAD4 genome AF: 0.0464 AC: 7066 AN: 152260 Hom.: 298 Cov.: 32 AF XY: 0.0450 AC XY: 3349 AN XY: 74448

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.0263

Gnomad4 ASJ AF: 0.0375

Gnomad4 EAS AF: 0.0118

Gnomad4 SAS AF: 0.0608

Gnomad4 FIN AF: 0.00188

Gnomad4 NFE AF: 0.0204

Gnomad4 OTH AF: 0.0454

Alfa AF: 0.0271 Hom.: 92

Bravo AF: 0.0500

Asia WGS AF: 0.0340 AC: 118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.9
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17057381; hg19: chr8-27416801;