rs17792746

Variant names:

• chr20-6378394-A-G
• rs17792746

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.284 AC: 11779 AN: 41486

American (AMR) AF: 0.263 AC: 4021 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1384 AN: 3468

East Asian (EAS) AF: 0.113 AC: 585 AN: 5172

South Asian (SAS) AF: 0.255 AC: 1231 AN: 4824

European-Finnish (FIN) AF: 0.246 AC: 2604 AN: 10580

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21280 AN: 67992

Other (OTH) AF: 0.316 AC: 669 AN: 2116

Alfa AF: 0.295 Hom.: 2644

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
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs17792746; hg19: chr20-6359041;