rs17057830

Variant names:

• chr6-129760528-A-G
• rs17057830

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 0.139 in 152,158 control chromosomes in the GnomAD database, including 1,710 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 0.14 (1710 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.714

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.215 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: 0.139 AC: 21135 AN: 152040 Hom.: 1700 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.0681

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0824

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.139 AC: 21164 AN: 152158 Hom.: 1710 Cov.: 32 AF XY: 0.136 AC XY: 10091 AN XY: 74402

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.0679

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.0824

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.155

Alfa AF: 0.117 Hom.: 1363

Bravo AF: 0.147

Asia WGS AF: 0.128 AC: 444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.042
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17057830; hg19: chr6-130081673;