rs17773813

chr4-55142802-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 0.252 in 152,040 control chromosomes in the GnomAD database, including 5,259 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 0.25 (5259 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.138

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38279 AN: 151922 Hom.: 5261 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.252 AC: 38272 AN: 152040 Hom.: 5259 Cov.: 32 AF XY: 0.250 AC XY: 18562 AN XY: 74318

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.259

Alfa AF: 0.280 Hom.: 785

Bravo AF: 0.244

Asia WGS AF: 0.201 AC: 699 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.8
Dann	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17773813; hg19: chr4-56008969;