rs17792746

Variant names:

• chr20-6378394-A-G
• rs17792746

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 0.289 in 152,132 control chromosomes in the GnomAD database, including 6,529 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 0.29 (6529 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178

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 (NFE) allele frequency at 95% confidence interval = 0.309 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: 0.289 AC: 43900 AN: 152012 Hom.: 6531 Cov.: 32

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.289 AC: 43910 AN: 152132 Hom.: 6529 Cov.: 32 AF XY: 0.282 AC XY: 20948 AN XY: 74366

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.399

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.316

Alfa AF: 0.291 Hom.: 2060

Bravo AF: 0.287

Asia WGS AF: 0.209 AC: 726 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	1.3
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17792746; hg19: chr20-6359041;