rs17773813

Variant names:

• chr4-55142802-G-A
• rs17773813

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;